I don't think this is really the right way to look at it. Shanahan's system makes it so easy on the QB. Any time Jimmy got in a situation where things weren't easy last night, he failed. Feasted on quick hitters and PA where his initial read was open and almost literally couldn't complete anything if he had to actually read the defense or throw the ball down the field.
He was better during the regular season than he showed in the playoffs this year, but at the end of the day, much like how the Rams made a mistake in paying Goff, San Fran has a system that almost any QB will be able to be successful in. There's no need to spend top dollar on an average at best QB with the system Shanahan has in place. It's fine for now; they don't need the cap savings yet so there's no need to restart at the QB position in the immediate future, but when it comes to the point where they basically have to either keep Jimmy or keep everyone else, they should definitely go with the latter. So I would be trying to lock in a rookie QB salary that you can develop right now.