You need to understand the situation a little more. Call me an Intel shill if you want, but here's some cold hard facts...
1. AMD is not overly compatible with FreeBSD. It's never been a great match with FreeBSD at all from what I've heard. Yes, it has worked. It has never been a flawless experience across AMD's product line because AMD doesn't have the revenue and income to pay devs to write code to make FreeBSD work on AMD builds. Just to compare, Intel's monthly R&D budget exceeds AMD's yearly budget by 5 fold or so.
2. Back when AMD was in its hayday (2004-2007 or so) AMD used to participate more in FreeBSD. AMD had paid developers (just like Intel has paid developers). Since AMD has basically slowed their support of FreeBSD (and all server-side stuff) naturally you can expect that over time FreeBSD will be less and less compatible with AMD systems.
3. Intel sells their hardware as a platform. 99% of the decisions are made by Intel, so Intel provides a pretty common experience on a given CPU. AMD doesn't provide the same kind of integration. AMD systems are usually an AMD CPU with one of a dozen or more chipsets that have been designed to work on AMD. Those chipsets are made by companies that do what they do while cutting costs everywhere they can. Even Intel based systems with VIA chipsets are a horrible choice for AMD, so this isn't "just an AMD" problem. For Intel though, non-Intel chipset based systems are in the extreme minority and mostly are the lowest end purpose-build hardware. AMD's entire product line is mostly things that are similar to VIA chipsets.
4. Intel provides most of the engineering specifications AND implements them via the BIOS. AMD's systems, by comparison are a situation where AMD provides options and the motherboard designer choose what they want to use or not. If you want a more feature-packed and more compatible system, you're going to have to spend more money. PERIOD. Of course, people buying AMD aren't looking to spend more money, so they are often left in the cold.
5. I don't know where you get your stats for AMD usage in servers, but they've NEVER been a "significant market share". Check this out...
http://www.businessweek.com/articles/2014-11-06/amd-falls-further-behind-chip-rivals-intel-qualcomm AMD had yet another round of layoffs just 60 days ago and fiancially they are VERY bad off. They may not exist by this time next year. Can you really be upset that support is poor for a company that *need* to provide support for their hardware. Unlike what most people thing, x86 is not x86. CPUs are far to complex to simplify things down to that. Having thorough engineering teams, coders that provide code, and proper implementation of features from inception to execution is vital. None of those 3 things are in AMDs favor, not even slightly.
Quite literally, when you buy AMD you are doing nothing more than supporting the underdog. Unfortunately the underdog is so sick right now you
shouldn't expect them to support you back. If this is unpalatable I'm sorry. That's the harsh reality. There's a reason why I've been labeled an Intel shill. The objective evidence suggests that AMD is an extremely poor choice for an obscure OS like FreeBSD. On Windows AMD might fair better. But this forum doesn't deal with Windows except on the client side, so that argument is totally invalid for the scope of this discussion.
So you can say that it sounds like iXsystems is developing away from AMD. It's more appropriate to say that AMD isn't really designed for FreeBSD. I've been saying this for more than 2 years. FreeBSD is basically continuing development, completely exclusive of AMD since AMD isn't participating. You could say that FreeBSD is outgrowing AMD and AMD doesn't have the friendly relationship with FreeBSD they used to.... mostly because of costs. Nobody would argue that FreeBSD should just stop innovating since AMD doesn't want to play. They just aren't enough of a marketshare to even consider making that argument.
At the end of the day, argue all you want.
AMD has not historically been and likely will never been a major player in FreeBSD development and support. Don't like that reality either don't use FreeBSD or don't use AMD. I'll let you decide which you want. But trying to argue that AMD has *ever* had a great relationship with FreeBSD is a laugh and a half for the rest of us. It's not even remotely true.
When I buy a desktop I care about things like chipset specs, on-board components (both type and quality), and actual hardware quality (such as manufacturing process). When buying server-grade, you are looking for a totally different set of variables. Unless you've been building servers for years, you probably aren't overly privvy to this info and it seems very non-intuitive. My first FreeNAS box (built solely for testing and never had real data) was only using recommended hardware because I happened to have an X58 based system collecting dust. It's circa 2008 and boots FreeNAS 9.3 without fail.
Now, changing subjects a little...
gpt issues aren't in the FAQ because the bottom line is that gpt support is very much a BIOS thing (as you've pointed out). So if it doesn't work, it doesn't work. There's not much option. I will say that Intel systems that meet our general recommended hardware work just fine with gpt. Why? Because that's well supported and "just works" as designed and documented. If it's not working for you then you're generally looking at something specific to your motherboard. There's just no way we can have support for all motherboards out there, nor are we interested in it. I know that the recommended hardware thread that I wrote and is maintained works just fine. If yours doesn't work then all I can really recommend is you stay on the more beaten path. That, by definition, means Supermicro stuff on an Intel-based system. If you were a FreeBSD wizard you might know how to troubleshoot the problem. But as your hardware isn't working and virtually nobody here even has your hardware, we don't really want to spend stupendous amounts of time on hardware that really isn't a particularly great choice, even if we *could* get it to work. When 9.3 was in beta testing quite a few AMD systems were found to not work. The answer was "talk to your motherboard manufacturer to troubleshoot the issue". Now a company that is selling their systems at cutthroat prices isn't going to be ready to throw tons of time and resources at a problem experienced by a small minority. In comparison if the X10 series (Intel-based) suddenly didn't work with FreeBSD 9.3/FreenAS 9.3, Supermicro (and Intel) would be VERY interested and willing to spend resources to troubleshoot the issue. AMD (and companies like MSI and such) don't make lots of money from your one board and are not overly motivated due to market forces to dig into troubleshooting the problem, nor fixing it. All that being said, feel free to troubleshoot your problem on your own. FreeBSD/FreeNAS is open source and code that makes your hardware work is gladly accepted. Being that you aren't a developer and may not have the experience to troubleshoot the problem, you're left with only one choice.. buy what you KNOW will work. That means AMD should be avoided.
Lastly, you need to understand that FreeNAS prior to 8.o was developed by a different group of people, had different engineering considerations, and is not related at all to the pre-8.0 except by name. PERIOD. So your argument about the FreeNAS working previously on "ancient hardware" isn't valid. The reason is that we do not and haven't targeted that market in more than 3 years. If you are yearning for the "old" FreeNAS that was designed for ancient hardware you should use NAS4Free. That is the true renamed project that continues fro the pre-8.0 code.
In conclusion (and I apologize for the wall of text, trying to explain things to you) I think your expectations of what FreeNAS is compared to what it was 4 years ago is outdated and the development of FreeBSD to work with AMD hardware is in AMD's ballpark and not FreeBSD. FreeBSD gladly excepts code from anyone. AMD just isn't a major player and not overly involved with FreeBSD. Even some of my friends that use linux heavily have said that AMD's support for linux has seriously waned in recent years, and there's serious concerns that linux may not be AMD friendly in the future.
At this point you should probably stop and ask yourself if AMD really is the way to go considering all of this information. I've never recommended them for servers in my 3 years here and right now I don't expect that to change. AMD is going to way of ARM for their future, so I expect AMD support for server OSes (and especially FreeBSD/FreeNAS) to die a slow painful death while people hold onto the past where AMD may have worked (for various definitions of "worked"). Just like 9.3 has been somewhat hostile to AMD because AMD hasn't added to FreeBSD development, I expect FreeNAS 10.x to be even more hostile. Unless AMD pulls it around (not likely considering the markets) I expect that soon no AMD hardware will work with the, then-current versions of FreeBSD in the future.