So, this appears to be a fairly common question when it comes to CSE2 and its forks.
RetroArch, and most specifically LibRetro, has a lot of requirements for implementation. Since the intent is that every core operates purely as back-end so Retro can serve as front end (and abstract away some problems such as controller customization), building CSE2 to comply with these specifications would be a rather time consuming task. Clownacy (the main developer of base CSE2) already tried some time ago and didn't get too far.
Furthermore, due to the nature of CSE2 being reverse-engineered code, it cannot be licensed as open source. This limits its availability to be distributed for open source distros and applications. This is compounded by the fact that RetroArch has an already available, open source engine for Cave Story: NXEngine. So even if we got thru the chore of implementing support for RetroArch, we can't guarantee that it will be added to the library.
Due to these factors, I have decided to not commit to a RetroArch version of Tweaked. Maybe down the road I'll try, but as of this moment it's not in the scope of the project. I know some people have shown interest in porting base CSE2 and potentially Tweaked on their own, however.