I think what you stated about patchwork success is the reason. I think Gibbs is viewed on a somewhat higher level as a coach than Walsh for what he did with the various teams. Not that it is that much higher because Walsh is considered brilliant for both his coaching and personnel decisions (drafting).
But the 49ers, I think, are viewed as a stronger organization during that period because they were able to put together a team that had personnel consistency for the better part of a decade. And that is something the public can relate to. Pretty much only Washington fans and NFL people can appreciate what Gibbs accomplished in his first tenure with three different quarterbacks and a totally ragtag team of players intermingled with some great players.
I'll say one thing about true Niners fans that watched them in the 80's and early 90's (same thing I told my Dad) "There are fans of 31 teams in the NFL who have a right to b**** if their team looses, you're 32."