Realistically how often are those two buttons actually used? Some may use them a ton, I get that, but I doubt they get a whole lot of use from the majority. Personally if I'm shuffling, it's done directly from the album, artist or playlist with Shuffle All and not once I'm in the controls screen. Rarely, if ever do I repeat the same song back to back, so for me that button is almost never used. With that said, I prefer them how it is. Just slightly out of the way and not in my view when I don't need them. Fewer things immediately on screen is cleaner.
It may not fit your use, but Apple doesn't design for the 5% (not actual number) they design for the majority. Your disagreement on it doesn't make it universally bad or a fact.