Perhaps release the mkv with DD audio tracks as standard and make the DTS-HD MA available for muxing?

I'd put the DTS-HD MA tracks as standard on the blu, however. If you're rocking blu ray, you should also be rocking DTS of some sort. Any receiver (of worth) made since well before the advent of blu ray should support DTS, surely.

And, yeah, worse case scenario: there's always the option to have the player decode the DTS for you (which you would already be doing, I should imagine).

That said, I have no preference. If there's room for duplicate Dolby TrueHD and regular DD tracks, without sacrificing video quality, then I don't see a problem in going that route.