I would say you are spot on. The one picture where the piston rod is pushed through the strut housing assembly it clearly looks to me that they were assembled incorrectly and you are spot on when you say that the washer was installed incorrectly. If they did the one incorrectly I would be willing to be they did the other the exact same way.
I made that mistake the very first time I installed the Bils on my truck. Took it for a test drive, knew something wasn't right, posted in the forums, realized I was an idiot and made the common mistake of putting the washer directly under the nut. So ripped them all back apart and did them a second time. Fun times!
If memory serves me correctly when I disassembled the factory struts there was a washer under the nut. So your shop is not wrong in saying they assembled them the same as the factory came apart. Unfortunately, in doing so they did it wrong. Per the instructions that came with the shocks.
I would be requesting that they replace the Top Mounting Plate and Bushing. If you can trust them I would also ask them to inspect all your Lower Control arm Bushings and Ball Joints. Mine is in the shop tomorrow having them all replaced with 97k miles on them. Hate for them to put it all back together, perform another alignment, and then you find out some of your noises were also because of LCA bushings and lower ball joints.