Maybe it shouldn't happen, but no one has gotten into the playoffs with more than 1 loss. And Alabama and Clemson have 5 of the last 6 national championships. They are the best two programs in the country without argument.
People hate the Yankees, hated UCLA, hated the Celtics...yada yada yada. I not a fan of either team, but I know what greatness is when I see it.
Should the FBS playoff change formats? Absolutely. Will it, probably. Would Alabama and Clemson still get in? Yep.
If the playoff is designed to put the best however many teams in a bracket together, Alabama and Clemson are in...until they prove otherwise. They are the best two. It has really never been about the best record. It's about whos the best. People struggle with this.