Actually, none of the libretro cores use a configure script. As you can see there is no configure step, it just compiles a makefile that's already in place in a subdir. You'll need to define what you need there.
My scripts to launch RetroArch assumes Intel (DRM/KMS) hardware and switches to a virtual console before launching the game. I'll revise this and put up a new build.
In the meantime, although a bit cumbersome, you could log in with SSH and do a "chvt 1". Your game is probably running fine in X.