If ND goes 12-0, they won't be frozen out of the NC.
Boise is a toss-up.
We already have the SEC trying to get rid of limiting 2 BCS bids to any one conference. The plain truth of the matter is the SEC and the BiG are the drivers, not ND and certainly not the Boises (although I cheer for them like crazy when they play in a BCS Bowl).
With both the SEC and ACC going to 14 and the BiG and the Pac at 12 (maybe even the Big 12 if it survives) there is way more power in terms of Alabama, Michigan, Ohio State, Penn State, USC, Florida, ad nauseum then the Irish by themselves have. These teams make the bowls, the bowls don't make them. As long as ND is available as an at-large, they don't need the Irish (who haven't challenged for an NC in a long time) to be part of a Plus One system. They do need the SEC, BiG, etc.
Even UT, who is probably the only single entity that is as or nearly as powerful as ND, has been forced to stand by and watch A&M head to the SEC, see OU and OSU flirt with the Pac without the Longhorns approval, Mizzou most likely going to the SEC, the LHN restricted in terms of high school content and the number of conference games allowed to be shown on it, etc.
Cheers,
Neil