The issue which I have bumped up against when trying to figure out how to use multitrack (or two channel) audio with Markers is the need to have some kind of tempo MIDI track alongside the audio.
Essentially, the issue is this: You want to go to an earlier (or later) part of the track, and that has a Marker to jump to. But what you DON'T have is a way for the audio to know when the end of a bar is, so that it jumps without a hiccup in the beat. You can set up Marker jumps in several programs so that it will jump at the end of the segment you are in, and that works quite well, but if you want to be able to jump at any time (as MIDI Markers allow you to) there is no way without a very accurate tempo track (especially on audio not recorded to a digital click, which rules out most everything from 15-20 years ago or so) for the program to know where the end of the current bar is...
But yes, some system for syncing Audio to MIDI, and deriving a super accurate tempo track from the audio, or at the very least a Region Jump system would be of great use to entertainers looking for a bit more flexibility with their backing tracks.
BTW, if using multi-track files with QMIDI is possible, a way to pitch transpose ONLY the pitched tracks (leaving the drums and percussion un-transposed) makes a HUGE difference to how good the transposed audio sounds. Some kind of system to flag unpitched tracks in advance and bypass the transposer software when the user sets a transpose would be a huge plus!
I know this is a big ask, but nowadays entertainers and shows are moving to multitrack audio and Markers in a big way, and a native way in QMIDI to do both these things puts the program on a far more equal footing to things like Ableton Live, etc..