Consider the fact that Howard wasn't playing with D1 talent so Bowden still had to do some coaching. If Jim Tressell lasts long enough to challenge Paterno, it won't bother me if his wins with Youngstown State are included.
Bear in mind that Penn State was an independent for years and feasted on Army, Navy, Rutgers, Temple, etc. over the years. FSU, rather than join the SEC, chose to waltz through the ACC for a decade before encountering any lasting competition from within that conference. Bear Bryant refused to play certain teams unless they came to Alabama or played at a neutral site. So there are plenty of caveats to be spread around.
If we truly want to compare apples to apples, we probably need to take the records and apply an RPI-type formula to see which coach has done a better job of getting his teams to perform well over the years.