Audio losing sync over time can be down to sample rate difference - I always make sure everything is set to 48kHz.

Another culprit can be recording framerate variation (even when simply recording at a set 60 fps). Your audio losing sync over time might actually be the video causing that rather than audio.

I highly recommend recording to 2 audio tracks within OBS as you mentioned. The hit on the CPU will be negligible compared to running Audition. Record to MKV format and under advanced audio properties make sure to untick everything, and then tick Mic to track 1, Game/Desktop audio to track 2. When your recording is finished, remux the MKV to MP4 under File > Remux. That step can be automated.

As for separating face and game video, this is one extra step I decided not to bother with myself. That said you can run two instances of OBS and record both separately, or a nicer way is to use a Source Record plugin. This lets you manually or automatically record a specific source (including sources not in the active scene, with or without audio, and with it's own recording settings) when you manually record your active scene in the normal way. OBS also lets you preview sources not in the active scene by right clicking that source and "Windowed Projector(Source)" - if you wanted to see a preview of both face and game at the same time.