Primitive Emacs Lisp functions are defined in C, yes, using helper C macros. There might be a way to extract the symbol names from those macros, and maybe enough information to generate the FFI bindings.

Any kind of rewrite of Emacs is going to be a lot of work, I am not denying that. But if we assume there is a layer where everything works as it currently does (the C primitives), the Emacs Lisp defined on top of that needs not be defined in C, as far as I know.

Also, the last time I checked, there were a ton of legacy stuff in the configure script for different platforms.