Yes they are, that's not what I'm saying. The scripts/build simply initiates the unpack, configure, make, makeinstall etc functions of a specified package. Libretro cores use static makefiles and some of these makefiles decide how the cores should be built depending on the platform variable. Your error indicates trying to use autoconf, but it's impossible to say what's happening as you have not included the full log either.
Looking at your change, I think the idea is sound. Makes it easier to support new projects.