There is literally no 2 loss team more worthy of being over a 1 loss team than Bama (who has beaten Georgia and smoked LSU on the road) over Miami who just lost to an ok GA Tech team who ND smoked.
But what did they do...precedent is set.
Its true the committee will not "unduly punish" Tosu for losing their CCG, which is why as a 2 loss team they would still host a first round playoff game, they just wouldn't do it as a higher seed than ND.
The only SEC team who could lose in the CCG and even still have a chance to host would be Texas, as every other SEC team would be taking their 3rd loss, but while 2 loss Texas might host as #8 seed they wouldn't be ahead of ND. Again, they won't unduly punish a 3 loss team for losing CCG, which is why as a 3 loss team they would still be in the playoffs, just not hosting.
You are correct about Penn State though..we should just get used to seeing them seeded ahead of us, as unless they lose another game or struggle really badly vs Purdue and then we absolutely destroy USC, they will remain seeded ahead of us.