Yes the firmware is slightly different on the Modular and Pedal.
The transistor inverts the signal, so when the input goes high it pulls the pin PB7 low. The Modular firmware configures an internal pull-up on PB7 and triggers an interrupt when it changes.
The circuit connecting to PB6 is for the trigger output on the Modular and can be ignored.
What you could do is copy the input circuit (one jack, 3 resistors and one NPN transistor e.g. 2N3904) and either
1) connect it to PB7 on the digital board of your OWL Pedal and compile a custom firmware version, or
2) connect it to PE2, the switch input, and use the stock Pedal firmware
with 2) any incoming trigger or gate will appear to the pedal as a button press. Beware that this also means that if the gate is long enough, it will trigger the pedal to change patch just as when you hold down the button!
If you want to try out 1) then I can perhaps help by compiling a firmware image if you like.