Ok, I found a way to do this with exclusions. It would be nice if this was an option in the future though - a checkbox on the Settings Page perhaps.

I used a few different ? exclusions:

*php?*
*/?PHP*
*/?s*

This seems to work ok. There is still one version of the pages in question without any parameters. I was afraid it might eliminate the page entirely but it didn't seem to.

As far as I can tell it didn't eliminate anything else that I didn't intend to eliminate. Its a little hard to tell with so many pages to skim through, but it looks ok.

Passing paramters after a ? seems very common and it's been an issue with other website tools I use too. Which is why a checkbox option would be nice to have.