In the build doc for the 3PDT-05 bypass board, there is a mock layout drill guide. However, it should use the image of the top of the 3PDT-05 board rather than the bottom so the LED is in the correct side for drill planning purposes.
Looks like it's an inverted view(bottom of pedal perspective). Could be confusing, for sure.
You guys are absolutely right. I've corrected the doc and PSD drill file in the zip and re-uploaded. Thank you.