nestopia can build a libretro core, therefore a "libretro" use flag should be added that optionally builds it. A libretro core is just a shared library (in this case, it'll end up at /usr/lib64/libretro_nestopia.so). To build it, "make && make install" needs to be run in the libretro subdirectory.
From current README.md: > Libretro notes: > The libretro port is no longer maintained in this repo, and is > now maintained by the libretro community. For libretro-specific > issues, please use the libretro repository: > https://github.com/libretro/nestopia