Part of what I've been wondering is touched upon in the response above..
Is it possible that almost all profile makers are, as a rule, completely ignoring room mics during profiling? It sure seems that way. And that could be a big mistake. While the room effect may not nearly fully transpose, other aspects still would and that may be playing a factor in what is missing.
Has anybody set up a rig in proper studio format, and compared a profile taken with and without the room/distant mics? To truly see how the final profile is being impacted WRT to the most natural result when compared to the reference amp?
Sonic
I haven't done as you describe, a proper test per se, but have tried profiling using a room mic. If I remember correct my issue with it was again quite similar to "normal" profiles. You loose reverb, but I'm not sure that's the problem with the tones here..