It's not the first bonus track, or at least I don't think so. It's the first HIDDEN bonus track. Some say that title belongs to Sgt. Pepper, but I think the run-out groove loop is a part of A Day In The Life, and is integral to the meaning of the song, so I don't call that a hidden track at all.
Anyway, I like Her Majesty right where it is. I don't think it would fit anywhere else on the album, because the rest of the album is so heavily produced with very dense sounds, and if it was put anywhere else it would be dramatically out of place. Even if they eliminated the gap between The End and Her Majesty, it just wouldn't work at all.