I don't think they'd sign him to be the backup. They'd sign him to the 53 man roster to be the scout team QB, so he can help them prepare for Dak, Watson, Maholmes, and Allen, and then Lamar in the playoffs.
Considering they're already wasting a roster spot on Cody Kessler, who I still don't know why he's here, since he can't replicate the athleticism of the QBs they'll be facing and he's certainly not a developmental prospect. If Kaepernick can still run and throw the football, and he's willing to play for the minimum, he could certainly help this team prepare for future opponents.
The thing is, I don't think he's willing to play for cheap and he's not going to take an offer where he doesn't have a chance to start. For that reason, I don't see him signing with anyone.