thanks for asking that, its question that i thought about alot during coding this.
short answer is: yes, its an either/or thing. if you use midi you lose the DMA, but you still have digidrums though for samples. supporting the various combinations of MIDI/native DMA/tuned DMA for the two channels would be rather complex.
the long answer is more philosophical: as i'm sure you appreciate maxYMiser is designed as a YM tracker primarily. as a result I've made several design choices considering the Atari hardware. there are other trackers that do the midi job well since they were designed for that (OctaMed etc) but would be pretty bad at tracking YM2149. restrictions in the atari hardware include memory, processor speed, programming language, number of channels provided by the soundchips, screen resolution and the number of hardware timers.
in the past i always refused requests to do midi out since the plan is not to make maxYMIser a full blown MIDI tracker - it would always suck at that. but on the other hand if you want to add an acid line or synth lead to your chiptrack this is now possible. hopefully it should be just the thing to add a little extra flavour to your tracks. also, if you have a plain ST, with no DMA, you can now get some milage out of those extra channels that were useless before.
its a compliment I guess that people like maxYMiser and Atari, find the combination smooth to use and want to do more stuff with the setup.