Matt, I think there is validity to your point. I don't concur with your assessment that it isn't close to Top 100, but I agree with the rest of it.
For years Interlachen and Hazeltine were perennials on the Golf Digest Top 100. To the rest of the country the Twin Cities were known as home of those two. Working and caddying there for a total of a decade, I can assure you that any visitors looking to see the best Minnesota had to offer contacted these two courses first. In doing so they overlooked Minikahda, Golden Valley, Somerset, North Oaks, Minneapolis, Oak Ridge, Edina, White Bear, and other very good courses. The perception, I feel fueled by the GD (pun intended) Top 100 list is that there is a falloff from Interlachen.
In reality there are courses that are either equal or just a quarter-peg behind ICC. You know the names by now. Golden Valley, despite some oddities, has always been my favorite from a 'most fun to play' standpoint. (Granted, if I played it as many times as I did Interlachen it may get old.) Minikahda, which I saw two years ago, is probably a superior golf course today.
One thing I can say to address the comment about the course not being stout enough to handle today's top males is that the par 73s in the Twins, mentioned in Confidential Guide as a uniquely Minnesotan thing, can easily be modernized. The 1993 Walker Cup was played at par 72 and Minikahda's card now reads the same. I've long asserted that if you took college players to Golden Valley and didn't give them a scorecard, they'd assume par 70 and walk off the course talking about those three hard par 4s. (As par 5s they are a joke in the modern game.)
Interlachen has something nothing else in Minnesota does...a remarkable history. Bobby Jones the year he won the Slam. Glenna Collette Vare in the Am during her prime. I believe the course was to hole another male Open that was scrubbed due to war. The club was awarded a US Mid-Am, swapped when Chicago Golf was unable to meet USGA membership requirements. A Solheim Cup and now the lady Open.
Minikahda is close, with I think two male Opens to their credit and a Walker Cup. The two courses are remarkably similar, although 'kahda finished with the short 4s and Interlachen gets most of them out of the way by #10.
There is no question that Interlachen is one of the clubs that benefits from the Tradition category. A great course, though, which you also mention.