Optimal motherboards are
server motherboards. Supermicro has a very comprehensive range, but there are other manufacturers. Asrock Rack increasingly does interesting motherboards. Gigabyte and Asus have server divisions.
Supermicro is a good starting point, but not the only option.
For what I see, the best option would have been a complete storage server, refurbished, instead of that Thermaltake monster.
I suppose that your woes were about installing extra trays/dividers and fans—34 of them, really?
Hm! BSD is NOT Linux, and there's no "RAID6" with ZFS. The equivalent would be raidz2, which is reasonably suited to hosting large video files. But your initial set of 14 drives would call for two 7-wide vdevs, which does not divide 64 (tough introducing hot spares could be a good idea at some point).
How many simultaneous transcodes?
Then return it, or make it your desktop.
1 is x8. With expanders it could drive the entire set of 64 HDDs.
2 is x16 (but could probably do with x8 electrical).
3: Let's assume x8.
4: Nice to have, but might not even be needed.
So, at least three x8 slots (or wider), one of which being open or mechanically x16.
In practice, x16 +2*8 will do, and just about any server board with C621 (or C622) chipset meets the requirements (save the odd mini-ITX board).
That's because basically all Intel CPUs are compatible—or were, before Alder Lake. For ECC, look at Xeon (some Core can do ECC, but you're outside of their league).