The over-arching problem might be related to the kernel and how it handles the USB bays, since this intermittent issue occurs with different drives, different cables, different bays:
Works under Manjaro, with LTS kernel 5.10 (so far, so good?)
Works under openSUSE LEAP, with kernel 5.3 + backports
Intermittent issues under Manjaro, with kernel 5.13
Does increasing the initialization wait time make a difference in the intermittent environments?
Does this problem occur with openSUSE Tumbleweed, with kernel 5.13?
I left out LTS kernel 5.4, since LTS kernel 5.10 seems to be working (and is a more recent kernel), plus you had boot-related issues with 5.4 (which is probably unrelated to this.)
What USB bays / enclosures are you using? It might be useful to others that are facing a similar problem.
I didn’t suggest to use Tumbleweed, per se, but rather to try narrowing this down to perhaps kernel 5.13 (or anything later than LTS 5.10). Since it worked on openSUSE LEAP (kernel 5.3), yet the same intermittent issues occur under openSUSE Tumbleweed (kernel 5.13), it’s safe to say that the kernel (above LTS 5.10) is likely the culprit, regardless of distro.
I have neither of those particular USB bays, yet I do have two other brands I might test this out on. I only use LTS kernels, so color me lucky.
Maybe this is yet another reason to stick with the latest offerings of the LTS kernels, and jump from LTS to LTS.
EDIT: As it stands now, using LTS kernel 5.10 seems to be the “solution”.