I don't think there is nearly the deliberate system like "moneyball" that exists within the 49er structure. That being said, especially over the last two years of free agency, (one of which is only a few days old), there have only been a handful of players worth (if anyone is) the insane money the top tier FAs get. Some other players have gotten huge paydays because it is sometimes necessary to ensure you land someone, but that doesn't mean they are worth it.
Our FO does seem to have an philosophy that keeping your own talent, which you can evaluate far better than you can evaluate other FAs and/or draft picks is a better investment and that the drop off between most big name FAs and the next level isn't nearly as big as their price tag if you get the right guy to fit your system. And/or that if it is, at least it doesn't hurt you as much if you make a mistake. The upside is a limited improvement, the downside is a limited loss, but the expense and potential long term limitation can be crippling if you overpay for someone who doesn't pan out at all.
Case in point someone like Braylon Edwards. Didn't really help, but didn't really hurt. However, committing a long term contract to someone like Albert Haynesworth (worst case scenario) can really hurt your franchise and FAs rarely live up to those huge contracts even under the best case scenarios. Those that do, are usually the ones who are retained by their teams, "franchise players", so to speak. Ones who switch teams rarely (not never) live up to the huge payday.
I think our FO is well aware of that and would much rather bring in 4-5 guys with potential at reasonable numbers and improve the team in multiple areas rather than break the bank on one player who if he doesn't pan out hurts the team across the board because of the money committed over the long haul.