why would the reversed phase be a problem for you in this scenario in the first place?
it is surely an annoying bug, I agree - but I´ll doubt that it´ll get fixed, the MD is 15+ years old now and hasn´t seen any updates in a while.
but in a normal setting where you´re not trying to double up on sounds, phase usually is not an issue at all, I feel like people are getting spooked by the word alone…
so let me put your minds at ease:
unless you also plan to record a “room mic” of your MD playing through speakers and mix that back in with the rest of your “drum set”, you probably won´t have any problems because of the shifted phase.
that is only ever really a problem when recording live drums/instruments with multiple mics, to my experience.
if you plan on layering samples and something phases/cancels out - flip-phase one of them, most of the times that´s all you need to do really.