Glad it wasn't just me. I threw together a board of a bunch of Donner Pedals, sorted by input dimensions.
If you look at the two on the left (or the two on the right), they have exactly the same size, are cropped well, but wildly different sizes.
Seems to be a bigger issue than just getting the pedal dimensions right or cropping.
-- HoboPelican
Sometimes the machines rebel and the automatism does not work. So see the note from further up:
So if the autocrop does not work uploaded PNGs that were edited with an external software indeed give the best results.
I have reworked the pictures, your pedalboard looks good now.