Yeah, I opened a ticket to ask about this when I had a team go into the semis that was ranked in the high teens, and finished like #14 behind many teams I'd beaten on the way. And it happened again last year to me in D1aa too, made the NC game and lost but ended up finishing 9th.
I was told head to head doesn't matter; the NC winner gets the #1 ranking and the other teams are simply re-ranked based on record and SOS. Doesn't matter who beat who. So even a deep run ldoesnt really matter cause, although your SOS gets better, so does everyone else's in the POs.