Audio separation? You mean capturing each app separately and mixing them on purpose? I think a "simple" upgrade to the next (non LTS) release is going to make it massively easier to do that.
(may not be so simple, depending on what else you've got on it already; if you end up re-installing from scratch, I'd recommend switching to
Ubuntu Studio, and then
installing OBS's official PPA as noted in the sticky thread in this section of the forum)
Pop!_OS is one of many derivatives of Ubuntu, so it inherits a lot from there. I think Ubuntu 22.04 LTS is going to be the last version to have PulseAudio. It was (and still is) a pain to use PA by default and JACK to go beyond the basics, with some apps only supporting one and not the other, and the need to bridge between them, etc., not to mention that PA and JACK are two completely separate programs trying to do somewhat the same thing while competing for hardware drivers that only allow exclusive access.
It's possible to make all of that work if you know what you're doing, but PipeWire makes it all obsolete by being drop-in compatible with both of them. It's a single program that manages all of the hardware and can talk to any app like PA does, while also connecting things like JACK does. It's the best of both worlds, plus a lot better compatibility with things like bluetooth, etc.
But PipeWire is new enough that the conservative Ubuntu community is only just now starting to adopt it. The latest LTS just missed it. The following release didn't. So if you want to stick with LTS, you'll have to wait a complete cycle to do it "the easy way".
Or if you want to play with PulseAudio loopbacks and bridges between it and JACK, there are lots of tutorials just a google search away!
Also, if you're doing anything beyond a basic volume control, I'd strongly recommend using a DAW (Digital Audio Workstation - essentially a complete audio console as a software app) to do all of the audio work, and then send the final result from there into OBS to pass through unchanged.
sudo apt install ardour
No matter what behavior you want in audio, the answer is probably, "Yes, you can do that." Once you have the tools, it's just a matter of knowing how to use them, which for something like Ardour, might take a bit of time and a few threads over in
that forum, not because it's hard, but just because it does so much.
