@iamjackslackof — IIRC It's to do with the caps, which store voltage. This is why sometimes when you first power up your board and hit a switch and it pops but then doesn't pop again the next time you turn it on (unless the next time is after powering down your board and firing up your rig again the next day).
Input is usually the problem, but sometimes the problem is how the circuit at the output interacts with whatever comes
after it. "Gee this pedal started popping after I moved it to be after my fuzz, and it never popped before..."
There are so many variables in play, and so many different standards that pedals are built to. Boss has a reputation to uphold and can afford teams of engineers, whereas a little one-builder bootiki type operation will build whatever sounds good and if your boutique pedal pops? Builder might just say "Gee it didn't pop with any of my gear or my friend's setup — we extensively tested it, must be something wrong with your rig."
Extensively tested = Tried it with a Strat and a LesPaul.
I think
RG Keen understands more and does a better job explaining it than I ever will.