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)
Yes I changed topic, but I didn't change concept. Your argument is that Michigan has the most league titles and therefore Michigan is #1 in the league. Ok, using that exact logic Princeton and Yale have the most national titles and are #1 and #2 nationally.
I would submit that excluding teams no longer competing is arbitrary too. They are part of the history so excluding them from their own history is arbitrary. Similarly, Georgia leads Florida in their all-time series by eight games, 50-42-2. Basically nobody believes that Georgia is a better program. Georgia leads the all-time series because they dominated up through and a little after WWII. Through 1951 the Dawgs led the Gators 24-5-1. Since then the Gators lead 37-26-1.
The same thing obviously applies to Ohio State and Michigan or to B1G/Big11Ten/Big10/Western titles. Michigan leads the M/tOSU series and has the most league titles for the same reason that Georgia leads the UGA/UF series, because they were better a really long time ago.
Over any current time-frame of more than 10 and less than 90 years Ohio State is #1 in B1G/Big11Ten/Big10/Western titles.
I do not believe that Michigan's pre-1926 titles are completely irrelevant but I strongly believe that they are VASTLY less relevant than PSU's, MSU's, tOSU's, and UW's titles in the last five years.
You started out by saying that "(T)he most meaningful stat for the conference's brass is to either be *the* team winning the most championships or at least very close." Then you stated that that was Michigan.
I disagree because "winning" is a term in present tense. At the present time Michigan is far from "*the* team winning the most championships", they aren't even close. In the last 12 seasons that would be:
6 Ohio State
3 each: Wisconsin, Michigan State, Penn State
There are 15 in 12 years because Ohio State and Penn State were co-champions in 2005 and 2008 while Michigan State and Wisconsin were co-champions in 2010. As you go back further Michigan catches the second place teams and moves into second place but they don't move into first place until you go back 91 years.
Using past tense, Michigan is the team that has won the most league titles but using present tense, for the past 90 years Ohio State has been the team winning the most league titles.