re: If PSU and OSU were reversed?

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The fact that a 9-7 Giants team was crowned NFL champ for beating the 16-0 Patriots, and only a month after the Patriots had already beaten the Giants in the regular season, shows the shortcoming of the NFL playoff system. It made no sense logically and proved how little the regular season means.

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The difficulty in winning the Super Bowl cannot be compared to winning a natty in CFB. Super Bowl >>>>>>>> natty and it isn't even close.

Additionally, the regular season has significant meaning in the NFL. shite the bed and you're out entirely. Don't win your division and you better pray you grab that wild card slot.
At the end of the day, no one complains about the NFL postseason because it isn't subjective in any way whatsoever.
Edit: Eh, someone will complain because someome always does.

Even those who come in with the poorer records generally have to deal with playing on the road, which is a very significant factor in the playoffs.

Furthermore, the NFL has parity where as CFB does not. That's why a 10-6 Giants team winning it all isn't some travesty. The teams that have a good chance of beating Bama is incredibly short.
The teams with a solid chance of beating the Dallas Cowboys includes a list of 31 teams. You can adjust for the Browns if necessary, but even they could play a complete game and win.

I'll take this a step further. Your point of "The Patriots beat them in the regular season" does not work in the NFL. There are 32 franchises and 16 games to a season. There are definitely going to be rematches in a system like that.