[noggin]

@wrxtasy
it's not the refresh rate app (that only changes resolution), what is interfering is the CONFIG_FRAMERATE_AUTOMATION kernel configuration, the one that gives buttery smooth 23.976fps playback.
The command that droidelec posted disables framerate automation so you will get the stutter every 41 seconds, but truehd and dtshd will work. This happens because that option alters the audio clocks as well.

If you ask me to choose, I prefer using multi channel PCM and proper 24p output, I really doubt that (I don't know what term to use, it's like in photography the person that looks every picture at 100%, "pixel peepers" but for audio ) anyone will notice a difference between multi channel pcm and bitstream, specially people using a Core.

What about leaving everything a 60Hz video output. Playing 23.976fps video with 3:2 pulldown ?
That was the solution I was trying to suggest, all be it not very well ...

if users need those fancy TrueHD / DTS MA / Atmos - smug "look at me" blinken indicators on their AVR's.

Wouldn't you get the same issue? If you output 23.976 content with 3:2 then you need 59.94 output if you want to avoid (additional) stutter. If you output at 60Hz you have similar issues to outputting at 24Hz. However I suspect 59.94 will have the same issues with HDMI audio clocks as 23.976?

(Personally I think I'd rather have stutter than 3:2 inflicted on me)