I’m a bit confused…
You should be able to tap any 5.1 signal at any point in the chain, so you can get the “5.1 file” anyway. If you’re routing via a send from one 5.1 output to another, then just select the first for the 5.1 file export.
As for the second, only getting L/R… Couldn’t you either just try what you said (separate channels) or route again to another set of tracks, but this time only L/R? Or use “child buses” or something?