In wins and losses Independent BYU is basically the same as MWC and WAC BYU, as you point out.
In relevance (ie, finishing in the Top 25) we fell off a cliff in 2011 and haven’t been heard from since. There are lots of contributing factors to that but our current stretch of ranking-less seasons is unprecedented in the modern era of BYU football. Everything stayed the same except one variable: conference affiliation.
We can continue to bury our heads in the sand about Indy, and pound our chests about how we’re now too good for the G5, but eventually we are going to end up in one of those leagues (or something like them) and we will all have to get over it. Some are just seeing the writing on the walls sooner than others.