I don't think it's necessarily tooling economies of scale, but probably custom-order costs-- rather than cranking out 5000 standard US QWERTY sets, you have to swap between five different toolings and run 50 sets of each. Even if tooling's free, there's a cost in the short runs and switching.
From what I've seen, a typical new keycap set is 90% existing tooling in a new colour-wave, and 1-10 completely new legends, usually that define the theme (there are seemingly 300 sets with Hiragana sublegends, but this one will have a Windows-logo key replaced with the Strawhat Pirate flag!)
I suspect there are efficencies to be found by pooling overlapping orders and reducing nonstandard kitting. Saying "everyone gets the 3/£ keycap" adds 20 cents per order, rather than making a few UK users buy a low-economies-of-scale kit at $25.
I've been fond of Maxkey's caps-- they seem to have achieved that accidentally. They seem to sell one basic cover-all set in different colours, and as a result they have pretty good supply and modest prices (their sets sell for about USD100, I suspect anything similar from Signature Plastics would cost 150 or 200, and have a 12 month turnaround)