Yes, you can update PP.
Either update the Python code that controls the tool setting routine, or update the low-level LinuxCNC pin definitions to add an inverter to the pin.
(Best might be to create a new pin that's the inverse of the existing tool setter pin, and then edit the python to use this pin instead of the original? Haven't checked the code in detail.)
The draw-back is that you lose your changes each time PathPilot updates to a new version.
You might want to store the un-hacked version of the code in a separate directory, and generate a patch of your changes using "diff -u" that you can then re-apply after updates.