IMHO saving money for less talent is a double edged sword - so the trade-off is a wash.
I think the biggest pressure is on scouting. Drafting late, you don't have sure-fire talent (as much as it can be -- a la Willis, VD, etc). You have to be able to "project" talent much better than your peers. Baalke and JH demonstrated that ability this draft with selections like Aldon and Culliver. So at least they may be able to do it better than most.
I think the primary advantage is the flexibility it allows you at the end of round 1 and top or round 2. You can make the case that the talent tends to break down approximately 1-15 top tier; 16-32 AND 33-43 of 2nd round are fairly interchangeable, as long as you aren't deperate for a certain position.
As a late round 1position, you have the ability to trade back with those teams desperate to fill a specific need and grab from a dwindling stock of 16-43 talent. Those trades are VERY lucrative too -- you can often get a next year's 1st rounder for one of these spots; or at least get their #2 spot and a 3rd and 4th in addition. This is the pattern by which NE stockpiles 1st round picks so often.
I don't see SF trading their 1st round spot this year because they have two glaring needs for upgrade - WR and C/G. BUT, if their guy looks to be available a few spots back, or they would take either of a couple of remaining candidate, let the stockpiling begin! That is how you build a dynasty in this day and age.
[ Edited by HearstFan on Jan 18, 2012 at 2:45 PM ]