Another option would be, wich already should be working, is to use a programmer, like esptool.py, read the memory block found on 0x3c(000) change it and write it back. The ssid and passwd are on the very start and occupy 32 bytes both (see config.h), be sure to add a '\0'! Maybe you can try that. If that's viable, I can add a config option to skip the bootstrap.
Another option would be, wich already should be working, is to use a programmer, like esptool.py, read the memory block found on 0x3c(000) change it and write it back. The ssid and passwd are on the very start and occupy 32 bytes both (see config.h), be sure to add a '\0'! Maybe you can try that. If that's viable, I can add a config option to skip the bootstrap.