First, if you have differences in some clips and no difference in others - then there are differences, period. They just don't always happen - for various reasons.
You know, perhaps better than most, what difference a cab/mic/preamp combo can cause - and that still has different interaction between poweramp and cab, which the Profiler assigns to the amp section, even with the newer FW.
Second, looking at your list...
333XL, 6262, Trirec, Fireball, 5150, Alligator, D-Rec, 5150, 6505, Satan, V2...
All 5150 variants, some closer than others.
The Hector, X100B, Triamp, GH100, Ironheart and actual Marshalls are all JCM variants.
80% of your list are variants of two different amps. When push comes to shove, most well known amps are variants of one another, circuit-wise and therefore also gain-structure-wise.
You see this as a limitation of the Profiler, i see this as a valuable lesson in electronics. I don't think you'd get different results by plugging the preamps into the same power-section, cab, mics and pres.
I do agree that more flexibility in poweramp-dynamics would benefit the Profiler greatly, but that's the only thing missing, for me.