What about the long bolt? That's obnoxious.

You can remove the wax, but all my toilets were installed with caulk at the base. Else centipedes harbor under there.

Some contractors are messy and just don't get it. You never know what you are going to get, and I learned SOME things you just have to shrug off.

I'd clean it up and ask them to caulk the base (provided they can caulk professionally). I'd first ask them to do something about that bolt.