Halfbaked idea: somebody should start a service where you upload a 3d design of a keyboard, including a mapping of keys to keycodes, and they will build the keyboard for you.
http://www.keyboard-layout-editor.com/
to design your layout, then
to design a layer case, files go to a laser cutting service,
then you would need a controller of some sort (commonly something like a https://www.pjrc.com/teensy/), switches, diodes, usb ports, etc.
then hand wire everything together.
tmk/qmk is more or less a defacto standard in custom keyboard firmware:
https://github.com/qmk/qmk_firmware
here are some examples of people generating firmware with webtools, I don't know what they use on the backend.