If it's true that the 90 watt Mark V is better at lower volume levels than the 25 and 35 (I don't doubt that it is, but haven't played a 90 watt Mark V in years), then it may be due to it having a real master volume control rather than just channel masters.
Comparing the 25 to the 90 I’d say the 90 is better for bedroom volumes because of the OUTPUT master knob to tame the channel masters. Plus, I really like the 10W mode. The 25 sounds good also but the volume knob is way more sensitive at low levels. If I was to only have one bedroom amp I’d choose the 25 to save some bucks. With gigs and such I’d get the 90 with 3 channels, lead boost and effects loop control.