I have no issues with any motors getting unusually hot, and I do pretty much exclusive command. I also have tons of locomotives on the bench testing at various times, and this has never been an issue.
The waveforms for command can be either PWM or the triac sawtooth wave, I don't see it making a difference. Since I don't have any "hot" motors, it's hard to narrow it down.
I'm going to do a test with a Williams A-A set I have, they're stock from the factory, a set that I always intended to upgrade... Since the contention is that the Williams motors get hot in conventional mode, that seems to be the most germane.