I have asked several schools this question and they said submitting more than the requirement is fine and that they will all be considered. Whether they actually sit and read all of them or not, I don't know. At schools that receive more than a couple hundred applications, I doubt LORs are really each looked at in any great detail anyway. As long as your references are all positive and from quality sources, you will be fine regardless.
Lots of people have to submit four even though most schools only require 3 or sometimes 2, because to cover your bases for a variety of programs you often need a professor, 2 PTs and an additional one from a professor/supervisor/employer/academic.
And no there is no way that I have found to specify which references you would prefer they look at the most.