The same thing happens in D3 in the regular season.
The issue is that schools budget to make such trips during the regular season. The NCAA would be footing the bill, presumably, for the bulk of the travel for the schools in a playoff system.
I think there are (and should be) legitimate concerns about appropriating a disproportionate amount of available NCAA funds to cover the travel expenses of teams participating in a D-1A football playoff. Using funds that way takes available NCAA money away from minor sports that need the organization's funding far more than major sports like football.
Thus, I think to accommodate those concerns, the NCAA would either have to have a major sponsor underwrite all travel expenses for its playoff or would have to adhere to the strict geographical limitations imposed on all other levels.
I went to find out how pairings are done in other levels. DI-AA has a geographical proximity requirement for the initial draw:
http://www.ncaa.org/library/handbook...l_handbook.pdf
On the DII level, the teams are kept in strict geographical regions and play through the region to reach the national semifinal level:
http://www.ncaa.org/library/handbook...l_handbook.pdf
For the record, here's the language applicable to DIII pairings:
http://www.ncaa.org/library/handbook...l_handbook.pdf