I don't think that's a use case the developers really envisaged.
I know under movies (and possible shows as well), you can specify versions:
https://jellyfin.org/docs/general/server/media/movies
But I think you're expected to select the version at playback time.
When I've had this issue, I've just transcoded to a format that all my targets can read without drama and kept the resulting file.
If your keen to experiment, I'd be curious to hear the outcome.