You are going to have traffic in Glacier. But it's not a nightmare. Totally worth the trip.
In general, I think the cautions are simply that: cautions about what you might encounter in certain places. For example, I did the section between Whitefish and Eureka mentioned above two years ago. Leaving Whitefish on U.S. 93 in the morning there was some traffic. Other than that, we didn't see very many cars on the portion of that stretch that uses U.S. 93.
That stretch of U.S. 93 had far less traffic than the section of U.S. 93 leaving Missoula on the TransAm. The shoulderless East Side Highway to Hamilton on the TransAm was almost non-stop traffic. I just rode both of these stretches this summer. The TransAm roads in Yellowstone were not exactly traffic free when I rode them in '00. Neither was the road connecting Yellowstone with Teeton Park. (I distinctly remember the map warning people to ride early in the morning to avoid heavy traffic periods in Yellowstone.) In contrast, the North Cascades Highway was nearly empty both times I rode it. Same with the other passes in WA.
You also have to consider what "increase" means. A road going from empty to moderately busy is an "increase."
Yeah. U.S. 1 was not the quiet country road, but I never felt threatened. iI you are there after school starts traffic will be lighter.
Yes. U.S. 61 in MN was busy in places, but I never felt threatened.
Yeah. There was traffic in Cleveland, but that's to be expected.
Ask yourself this: Do you think they would maintain a route that is an overall traffic nightmare? You list 13 bullet points. The route is what, about 4,400 miles? Doesn't sound too bad to me. I am milling to be there are 13 areas of the TransAm that could be described in similar ways. Indeed, I listed two above in a stretch of about 50 miles.