I'd also ask if the chainring mounting bolt areas were ever lubed. That's a common source of clicking that a little light oil or spray lube will fix.

The only time I had this type of clicking noise the real culprit was a rear skewer that needed to be tighter and/or lubed. It had nothing to do with the crank, but you couldn't tell that by listening. A shot of WD-40 and a lighter tighter setting fixed my problem.

The last possibility might be a crank that was actually built out of tolerance, but most shops won't have the measuring tools to check that. If the crank is installed without the wave washer and there is more than 2.5mm of axial play, then the wave washer can't do it's job and some shim needs to be placed under the left cup to get the axial play down to 1.5-2.0mm. That insures some compression of the wave washer.