Huh. I've never noticed that behavior (of everything syncing). I just use the sync button on the page I'm changing, which is usually Music, if anything. And, I've not noticed the auto-backup, either.
Well, that was my shot at a fix. I don't use syncing, TBH, mainly because I don't like iTunes's behavior if I go outside my "norm" - I only do "transfer purchases" and self-initiated backups. And, my auto-sync is turned off, also. So, if it still does the stuff you describe after being turned off - well then, now I am reminded why I don't sync.
And, yeah, I've noticed that iTunes puts deleted apps back on the iPad after a sync. Which annoying and yet another reason why I don't sync...! And, no, I don't know why it does that, either.
So, I've not been of help. Sorry. But - I can commiserate with you. Maybe someone else will be along who has a better idea about iTunes and syncing.
Marilyn