The average NFL team spends 18% of their cap space on OL. with a 122 million dollar cap, the niners would need to spend about 22 million a year on OL salaries to be within the norm. The good news is the FO has locked up both OT's until 2019 and the center spot is locked up until 2018. That leaves the Niners with Iupati coming up in 2015 and Boone in 2016.
The Niners can only afford to keep ONE of these fine elite OG's. Otherwise their salary cap distribution would be too heavily towards OL. I think THIS is the main reason BOONE is holding out, he wants to get paid now, and be part of the Niners. This would ensure Boone is around for hopefully the super bowl runs and Iupati will have to go in FA.
I actually would prefer Boone over Iupati as he can be the back up swing tackle if he needed to be.
This is just my opinion. But I do believe the niners cannot afford both Boone and Iupati.