I can't speak for the Niners but the Seahawks don't have a developmental QB waiting in the wings to become the #2 if Flynn is released (Wilson was supposed to be the developmental QB) and Wilson is on a rookie 3rd round contract so is dirt cheap. If Schneider is offered a high enough pick he'll trade Flynn. If not he'll return as the backup.
Having five rookie QBs starting at the beginning of the season is the exception, not the norm. I wouldn't be surprised if there are no more than one or two starting at the beginning of next season so that means teams looking for new starting QBs will need to find them elsewhere.