Just to clarify. Dolby Atmos is either Dolby TrueHD + additional metadata or Dolby Digital Plus + additional metadata.
First, can you check if you also experience the crash when playing a 2D file with a TrueHD audio track?
If your audio settings are default, that should mean that TrueHD passthrough is disabled, which makes it more likely that the problem I described is what you’re experiencing.
If you want to use Plex to manage your media and update the watched status etc. you can try PlexKodiConnect which many people think is better than the official Plex add-on. It uses Plex only for the backend, but still uses everything else from Kodi.
I wouldn’t get my hopes up too high because this issue has been around for some time and AFAIK it is not an OSMC issue but rather a Kodi issue. And according to this, it is not even being worked on atm.
If your TV is capable of decoding TrueHD tracks you could consider connecting the optical cable from your TV to your AVR. Then you could enable TrueHD passthrough and the problem should disappear. Of course then you would lose any surround capabilities because your TV will send a PCM stream to your AVR and optical cable only supports 2 channel PCM sound.
There is a guide for audio related settings.
Yes if you use the default Kodi player (which is also used when using PlexKodiConnect) then it should only crash on chapter skips (pressing up/down on the OSMC remote).