It has been my personal experience that the USB Flash boot device takes longer to format depending on its size ever since we have started to use the ZFS (GPT) format on the Boot Device and the only answer I have is something which sticks in the back of my head which says that the drive is performing a scrub but hell if I can recall where I read that. So either it's a scrub or formatting or both which is causing the delay. I'm certain that if the OP looks at the Flash drive activity light during this installation delay, that light will be flashing the entire time. And I know this concern has been brought up before in these forums and addressed, or maybe it was a bug ticket, I don't recall.
I think the only way to know the true answer is to look at the installation code or have one of the developers chime in.
And you cannot compare a high speed internal hard drive directly to a low speed USB device when comparing capacities. Most internal hard drives have some sort of built in cache and they are running at SATA speeds. Poor USB is so slow and a cache only exists on expensive USB devices (I do have one but I'd never use it in my FreeNAS machine, it's for financial data).
Lastly the Sandisk Cruzer fit 64gb has a slow write speed but a fast read speed (~8MB/sec write, ~20MB/sec read) based on results posted at
this web site. I have a Fit 32GB and my tests connected to a USB 3.0 port on my main computing system are: Seq Read = 36MB/sec, Seq Write = 25MB/sec, Random Read = 28MB/sec, Ramdom Write = 2.3MB/sec, Random Read (4k blocks) = 4.8MB/sec, Random Write (4k blocks) = .9MB/sec. So it's not a bad little device but you must take this into perspective and if the OP used a USB 3.0 enabled port or not.
My Conclusion... This is not a problem in the sense that because it is slow that something wrong/bad is occurring, it isn't.
At the OP, for your peace of mind, run a scrub on your boot drive and see that it passes and how long a scrub takes. Or you could use a different device. 64GB is a bit large in my opinion, not worth the cost for a FreeNAS project. Also, are you using both USB sticks you listed as a mirrored boot system or just the 64GB fit? I've never used a mirrored boot system but that too would add time into the formatting/scrub process.
If anyone has any first hand knowledge using a 64GB USB flash drive for the boot device and either had the same issue or didn't experience it at all, I'd like to hear about it. I'd say most of us are running either 8 or 16 GB USB sticks though and I'd think the 16GB stick users would have seen an installation time of several minutes.