A lot of teams have limited backups and end up with very short passing games. Its one of the reasons X and O Twitter is screaming about the stupidity of not signing Kaepernick.
However, even if the backup is capable, unless he has started before, the offense will need to change, even if the QB "knows" the offense. These guys aren't clones and run highly tailored schemes. So signing CK or running with an untested backup means there will be a few weeks of bad offense while they figure it out.
Unless you are the Patriots and have it all schemed out already.