If you are talking about the bad romset white screen that literally tell you to not report it, then DON’T REPORT IT, thanks. Instead, go read https://docs.libretro.com/library/fbneo/#building-romsets-for-fbneo like that message is telling you to.
If you are talking about real bugs, and not bad romsets the white screen is warning you about, you can report the issues in upstream github repo or on our forum, it’s actually the recommended method.
The libretro fork is deprecated, the libretro core is built directly from upstream repo, so yes flycast issues should definitely be reported there.