I can happily defend that:
First, you changed the topic -- twice. You switched to NCs and you left the Big Ten.
Second, if you insist on talking about all conferences and NCs**, there are a bunch of ways to reconcile it feeling "weird" that Princeton and Yale are on top. For that, feel free to scoot to the final paragraph. But my preferred method would begin here by ranking the NC getters by their rate of NC-acquisition (total NCs [FBS or Div.I] divided by years spent in FBS orDiv.I).
Adding context to those lists does not require a treatment with specially chosen years. Princeton and Yale left Div.I a looooong time ago. That makes their concentration of titles even more impressive than the raw numbers you reference. They were more dominant in their era than any team in any era. So if we rank all teams across all-time by their rate of NCs, of course they deserve to be ranked at the top.
Now, if you ask me to propose how to change that list (without changing its years) to make it perfectly relevant to today, I'd merely ask you to exclude all teams who are not currently in the FBS. Excluding Princeton and Yale in this way is quite natural. In many senses, they've already excluded themselves.
**(which I'm cool with, and it's certainly true I find the "all-time CFB" span the least arbitrary for those topics, too)