I've just accepted that the AXE models match Cliff's reference amps and how they were modeled (tubes, effects loops, master volumes, build date of the amps, loads, and all the other factors, etc.).
Only in the cases, and they are rare, where after a new firmware update causes an amp I know in the AXE to be way off compared to how it sounded prior to the firmware update (i.e. a bug with the new model) or Cliff discovers some other bug afterwards. Other AXE users generally catch these too and they are reported and fixed. The JVMHJS and one of the Diezels had this happen a few firmwares ago and they were reported and fixed.
After I did the tone match test where the controls on the BE-100 were exact compared to my amp 2018 BE-100 (which I believe is the same version as the AXE), I'm comfortable knowing that if I can get the AXE model to sound the way I want it to, then I don't really care if it the dials match (because they won't).
If you have the exact same physical amp that is in the AXE, and you want the AXE model controls to match exactly, tone match it against the real amp with all the controls on 5 and it should match. I'm guessing that there would be cases where the MV would still be off though comparatively. Otherwise dial in the AXE models until you like the way they sound.
I frequently have to use some combination of the Treble, Presence and High Treble pots in the AXE but I also like my tone with a little more high end.