You're forgetting one very important expense. Unless you can come up with a schematic for an awesome-sounding pedal off the top of your head, there's a fair bit of R&D in putting together a non-clone pedal.
The hard part isn't building things (though a few manufacturers manage to frak that up), it's coming up with a piece of kit that actually sounds good to a lot of people without sounding like every other box at Guitarget. After a builder drops a few hundred hours conceiving, designing, testing and tweaking, it might be nice if he actually got compensated for the time he invested in his creation. When sales volume is measured in hundreds of units per year, the per-unit cost of that R&D is steep. If people aren't willing to pay it, the builder either goes under or builds as a hobby. If the builder is sufficiently lucky/talented, people will pay a premium and life is good. . .at least until people start asking "Why do people pay so much for a few bucks worth of parts?" and cloners get involved.
That's one reason why rip-off builders piss me off: They don't spend their time coming up with a new design or even a new take on an existing one, they just duplicate someone else's hard work...and all too often, people reward them for their larceny. Much as I'm frustrated by builders who "goop" their circuits, I can definitely understand why they feel compelled to do so.