At some point in the not-too-distant future, there probably will be a middle tier between FCS and FBS. However, we're still talking 10 years down the road. Since teams don't really make money in lower-tier bowls, it would seem logical to assume whatever middle tier breaks apart would have some form of championship tournament. I fully expect the FBS to adopt at least an 8 team tourney within a few years, as the need will become apparent once the money from the 4-team playoff starts rolling in (plus, BCS bowls have steadily lost income and attendance since their inception; only the Rose Bowl and NC game sold out last year... the other 3 games didn't).
I don't think it makes any sort of sense for Eastern to start planning for something like this now. Besides, the Gateway Project really just keeps the program on equal footing facilities-wise to the rest of the Big Sky.