Fellow PA pede here. I was provided with a sharpie and questioned a poll worker when the ink bled through. I was told that the machine could still read my ballot and, when the machine accepted it, didn't think any more about it. My county shows red for the result so I don't know if it was actually an issue or not. Just sharing my experience.

Edit: I previously lived in a state with Diebold machines so I was just happy to have a paper ballot. It never occurred to me to read the fine print regarding writing utensils.