The cost of the PCBs must be driven by assembly, right? The board itself should qualify for JLCPCB's budget offer at least: 2 layers (judging by the KiCAD-screenshot), < 100mm, HASL, nothing special about solder mask or board thickness either from the look of it. I'm not not sure about the plated slots of the USB connector, though? Do these cost extra?
How many did you get assembled per version? Just two of the boards or all five of them? Did you try to stick to using the standard parts or extended library? Which difference would it have made to do some work on the PCBs yourself, e.g. by soldering the through-hole connectors by hand?
Either way, it is definitely an amazing project!
Edit: as soon as any part is from the extended library, all different components (even standard ones) incur a cost for loading them into the pick and place machine, right? So minimizing number of different components is the only way of keeping the cost down, I guess.