There's not quite a 1-1 correspondence between black and green DTS files. I wouldn't expect there to be, except where the hardware on the two overlap.
In this specific case, I noticed that while there is a am335x-boneblack-audio-emmc.dts, there's no corresponding am335x-bonegreen-audio-emmc.dts. It seems the boneblack one is equivalent to the am335x-bonegreen.dts plus two entries for clk_mcasp0. I assume the lack of an explicit am335x-bonegreen-audio-emmc.dts is just a minor oversight? I can imagine it gets unwieldy to try to have every possible .dts for each of the boards.
I just wanted to make sure there wasn't a more specific reason why the green version of the file doesn't exist.
I used am335x-boneblack-audio-emmc.dts, and it seems to work fine in 4.4.7-bone-rt-r9 (aside from the other audio issues that arise).