I know this has been discussed a few times. But I haven't seen a clear answer on it.
I'm ripping with MakeMKV and then compressing with HandBrake (normal profile defaults for audio).
The new versions of handbrake can pass through any of those tracks, but decoding/recoding into something else might be an issue.
I have MakeMKV rip EVERYTHING. In handbrake, I have it convert one track to AAC (compatibility reasons), then convert-or-pass-through an AC3 track (my playback works better with AC3), then pass through the "better" track(s) for when/if my playback supports them.
Of course, I'm not running the latest handbrake - I'm still using 0.10.3, because I don't want to put up with the non-FDK AAC encoder.
But that's a discussion for the handbrake forum....