I have never quite understood this argument. UGA fans made the same argument a few years ago.
The rankings are dynamic and are based on games played up to that point.
The team wasn't "penalized" for being on a bye, it's that the teams "resume" wasn't nearly as good as the other teams to that point.
At this point in the season, I do not put much emphasis on rankings.
I'll start worrying about them come mid to late November, as the season winds down.
There are still games to be played, and each one could impact the final rankings.
Right now, I see BSU being #3.
Assuming OU beats OSU later this year, the only way I see BSU making the NCG is for Clemson to take a loss.
If Boise St and Clemson both finish the season undefeated, I can see Clemson getting the nod over Boise St.