my point is that the "injustices" of a team losing a tie-breaker for the second spot in a conference championship game would hardly be unprecedented in the general history of college football.

I don't think it is very likely that 3 conference teams would go 8-0. Even more unlikely that three teams would go 9-0 (since we seem to be heading that direction). Think about the annual rivalry games. If we assume the 4 annual games the article defined for the ACC, every year there games would happen (for starters):
FSU - Clemson
FSU - Miami
VT - Miami
GT - Clemson

So... if FSU is undefeated, Clemson and Miami could not be (as well as GT and Wake). VT could also be undefeated (meaning Cuse and UVa would not.) Louisville or UNC could also right? It COULD happen... but likely? Nah.

And even if it did... the top two playoff ranked teams would play and third would be out. It's likely the third team would be lower ranked because it lost an OOC game or two. How likely is it that 3 teams in a conference go 12-0?

I wouldn't lose sleep over it. And I certainly do like the idea of dropping annual games with non-rivals for a more inclusive conference schedule.