The frame animations do match one-to-one, with the sole exception being that there are some pickups that have two frames in the MD5 whereas the original MDL only had one.
I haven't been able to determine why.
But otherwise, I did go through the whole process of comparing every single model's frame count with the originals.
I believe that the re-release QC has recently had a GPL release so it should be possible to investigate further, check the animation code and frame definitions, and even figure out what that pesky extra frame in those pickups is.
(Yes: available here: https://github.com/id-Software/quake-rerelease-qc
- I'm a big advocate of actually reading the original code where it's available, rather than try to reverse engineer and make mistakes.)
Down-converting MD5s to MDLs seems to me to defeat the whole purpose; it would have been much nicer to see wider uptake of MD5 support in source ports, and I'm at a loss as to why it didn't happen.