This is weird.
If he was signing a one year deal with a team in order to get a big contract, it seems to me that it would be wiser to join a better team so that he can take advantage of the natural bias people get where they think players are better than they are because they are on a more visible/winning team.
Also, considering the strength of the 49ers line that really helps the secondary. Not sure you can rely on San Diego to bring the same quality of a front seven to push the opposing QB into mistakes.
As for whether a competitive NFC West would be a reason to run to another division? Not sure that makes sense considering the QBs are not the primary weapon of most the teams in the NFC West like they are in other divisions, and the NFC West is generally strong because of the stellar defenses.
Maybe NFL GMs are smarter than that (but we know this is not true), coming off a strong team after a good run the playoffs seems like it would get you more visibility. It seems this is what you would want going into free agency. Not saying the Chargers are bad, but they won't be in the spotlight like the 49ers and if the 49ers secondary improves Flowers would be in a good position to take credit for a lot of that.
Weird choice. I wouldn't want him on the 49ers but I cannot see why HE would not have wanted to join them. Was it all his choice?