I'm not sure I follow. If it's a matter of Wave Agent not allowing renaming when separating, I don't know. I'd ask Sound Devices. I don't know if there is a way for Wave Agent to otherwise know how to name tracks on the polywav to match the inputs you used and which are the stereo mix.
You're not the first to ask for this. AFAIK, the polywav won't contain such information - or SD won't do it.
If you arm inputs 1 & 3 and record those with the stereo mix, you get a 4 track polywav, 1,2,3,4.
If you arm inputs 2 & 4 and record those with the stereo mix, you still get a polywav with 4 tracks, 1,2,3,4.
If you only record the stereo mix, the polywav is just tracks 1,2. How do you label it as tracks 7,8 (on a MixPre 6), and how do you know it wasn't inputs 7,8 on a MixPre10? It would also be nice to mark tracks recorded in stereo. Keeping notes is a small price to pay for the capabilities at this price and size. I just avoid Wave Agent and explode directly in Reaper, then follow my notes and relabel/manage the Reaper tracks, no big deal and it's never more than 12 tracks.
You should ask SD. It would be interesting to hear their response. Maybe the 800 series does this.