Because so many of our players have emerged as stars/pro Bowlers, we are headed for salary cap hell in the next few years. There will not be enough money to keep everyone. This is why even the best teams have holes in their lineups; there simply isn't enough money to have top players at every postion. Under Singletary, the 49ers benefitted from having top talent, but the team didn't play well. Harbaugh's staff arrives and gets this talent to play well. Now these players have value they didn't have before, and when their contracts expire they and their agents are going to want to cash in as free agents before the become so old that their talents diminish.
To finally make my point, this is why I do not think the team keeps Alex as a backup. They will need that money to sign a valued starter who would otherwise become a free agent.
Some still like to contend that Alex is not top 10 quality. I respectfully disagree. For years, the QBs that are generally accepted as top 10 happen have also been in the top 10 QB rankings. Some Alex-dislikers are saying that the rating system is a good measure of QB talent, EXCEPT when it comes to Alex. Bull! While it is true that Alex's spot this year is helped by Roman's game plans and the OL and WRs they have finally put into place, that can also be said of practically all the other top QBs. They, too, have good coaching, OL and receivers. The league is too tough for a top QB to excel if the other pieces are not in place.