"All my devices that don't support TrueHD play the AC3 track correctly "
Apples and oranges.
If there's more than one audio codec that a playback device supports if the file format supports multiple audio tracks regardless of the file format for the archived video you still have to select with audio track you want to listen to.
If your playback device only supports one of the two audio codecs it doesn't "see" the non-supported codec in the first place.
Nothing about MKV or M2TS is any different in terms of how they perform during playback with multiple audio tracks. They aren't the controlling factor assuming multiple audio codecs are present and the playback device can see those codecs.
If you are connected to your PC with HDMI it has nothing to do with playing the Atmos track. The SOFTWARE you are using for playback on your PC does.
If you are connected via optical, coax, etc., you won't get HD audio no matter what.
If you want Atmos playback from your PC you need to be connected HDMI to a receiver that can do Atmos and using playback software that allows the pass through. Most do, like the free Media Player from DVDFab.
E.B. White said, "I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day."