The only way the mirco can tell the bypass switch is closed is to have PC5 become an input. That’s what exactly is shown in the fourth trace, that pulse with the rc decay is the pin changing from a high output to an input with its pull up enabled. The first trace shows the same thing and the differences in amplitude is change in PC5 from output to input.
If you use two channels and observe both port pins at the same time, it will make sense, you cannot see them independently with just one input channel used.