For me it completely depends on the thickness of the feet. If they’re quite thick/deep then I’ll remove them but keep them in the pedal box in case I want to put them back on at any point (for resale etc) but if they’re quite thin I’ll often just slap the Velcro over them. Ultimately, you want the most amount of surface area contact between the pedal and the board, so feet which are too thick will mean that vecro applied over them will only really attach at the four corners of the pedal and not across the rest of the pedal’s base, if that makes sense.