Better achievements are better achievements, regardless of when they occurred. I don't see anyone claiming BYU is on a tier with USC or Notre Dame in accomplishments but when it comes to football their achievements do far outshine Utah's. Doesn't mean that as things sit today BYU has a better team, they obviously do not, but it does mean that in the world of college football BYU has superior accomplishments and superior achievements over the life of those two respective programs.
And yes as a brand BYU occupies a higher tier than Utah does, there are a lot of factors why that is the case but it is just the way it is.
Once again that doesn't make any specific team BYU has better than any specific team Utah has, those things are fluid, but brands and legacies are built over time and because of the national championship, national awards, all American's, rankings, and other things BYU has done on a national level their brand is a much more recognizable and marketable brand.