Rockne's 105 -12- 5 record is by far the best winning percentage (86%) in college FB history
Bryant was 0-4 against ND and he didn't even face ND's top two coaches of all time Rockne or Leahy, who won 4 NC's in the 40's.
So yes in theory you could conclude that Rockne or Leahy would have beaten Bryant.
As far as NC's, ND ONLY recognizes consensus national titles (11). For example, Rockne had 5 undefeated teams and all five squads were named NC by various polling organizations. ND however, only recognizes the three Rockne squads which were voted #1 by EVERY polling organization, and back then there were a LOT of them.
If ND counted every squad that was voted #1 by at least one polling organization like most schools do, they would have 21 NC's.