I'm very concerned by this thread, as I bought two MS-01s, and two TL-D800Ses, both running TrueNAS Scale, and am planning to buy have purchased two more MS-01s and two TL-D1600Ses, to also run TrueNAS Scale. I have the same memory and CPU option as OP. I'm using the HBA that came with the QNAP JBOD, in both cases.
I'm running bht now (one unit has 8 x 8 TB drives, the other, 8 x 6 TB) ...
Edit: bht has done two complete sets of write, then read, passes, on my 6 TB drives. It reported one error, on one drive, at ~81% of the way through the first read pass, and nothing on the second. It's about 25% through the second read pass on my 8 TB drives, and no errors have been found on any disks yet. It doesn't look to me like I'm having the issues that OP did. It seems I am having the issue, just not to the extent that OP had.