As multiple folks already said, passthrough doesn’t manipulate the audio, so nothing has been stripped out. It passes it through directly to your file, unchanged.
(Also, if you can’t hear the difference yourself it seems academic, IMO).
Handbrake still has “Dolby Pro Logic II” and “Stereo” settings. It’s just that newer releases now default to Stereo for the “mixdown” instead of DPL2. Probably because of the same pointlessness Juice mentioned for most users.
The documentation on the website hasn’t been updated yet, but if you read the Handbrake changelogs you can see the change.
tl;dr
You haven’t lost anything when you use passthrough.
It IS just stereo. So it’s identified correctly in Plex.
I think you’re confusing track name/track metadata for an actual change to the actual audio. It’s not the same.
For that reason, since Plex doesn’t actually display track names (although that would be nice Show names for audio tracks and subtitles) you’re not going to see “Dolby Surround” in the list.
If your system can interpret Dolby Pro Logic you can benefit from the “extra” channels (which seems to be what you’re describing). Even if it’s just a mixture of marketing and ventriloquism.
The original format is “lossy” so there’s no “loseless alternative”. But literally any other options except passthrough can only result is additional loss of quality, although for most of us it would probably be imperceptible if you use decent settings.
