I'm still seeing a supply timer reset when 2 unsupplied vessels undock. Its always the crew of the unfocused vessel.
While I was testing that, I thought of a minor exploit. It's probably not worth added complexity to deal with, but I'll throw it out there. Since docking recalculates and resets the short term habitation timers for the entire crew of both vessels, one could do something to get a large long term timer and then use docking to reset the short term timer.