Build Espruino with user code

Yes, there is - use the Espruino command-line tools (https://www.npmjs.com/package/espruino) with the --ohex option - there are some docs for it on that page.

It depends a little on the MCU you're using, but if you're using nRF52 like most people seem to then you can just use normal tools used to merge the softdevice to merge the generated hex file.

Or... You can just set one device up how you like it, read back the contents of flash into a file, and write that file to everything.