In Redacted, this is a non-issue. In fact the default way capsules are sorted in Redacted, is by acquisition.
In Prime, it's simply not possible to sort capsules and/or "key lockers" by acquisition; they are always sorted by name.
Have you used the capsule renaming? I find no need at all for the old sort orders because I can name them all exactly how I want for the exact order I want.
etc, means my Quantums are always in the exact order I expect **even if empty** !
The same goes for any plain capsules I've name, and for Key Lockers.
What you can't do is control the order of them all at once with this method. No matter the name it's always:
Quantum Capsules (named or not, I've not had an un-named one in a while to check where it would be)