I was able to roll back to the 12/19/23 version 2.9.2.49629 and ran the 1200, 12,000, and 30,000 foot tests again and got the same results; the traces matched each other almost exactly and well within any sort of margin of error. The only difference I found was that the jet could reach higher speeds in MIL on 2.9.2.49629 than it can now in 2.9.3.51704.
First value is full MIL in previous version 2.9.2.49629, the second is full MIL in current version 2.9.3.51704:
1200 FT: .97 vs .95
12,000 FT: 1.02 vs 1.0
30,000 FT: 1.13 vs 1.08
The results still don't make any logical sense to me, especially in the FPAS curves, where usage abruptly just levels out and starts to decline. Though, as I said, I don't pretend to understand the math or theory that governs fuel usage. I think the other changes in the FM were enough to have me take a closer look at fuel usage, as it seemed different now, which, as it turns out, is not the case.
KLaFaille's post in Fuel usage inconsitencies at varying speeds and altitudes since FM update was marked as the answer