Thanks for the reply @bob493 .
I'm pretty sure the neck on my 560 and 450 are interchangeable, that's why I thought it was weird that it didn't quite fit the new body. I mean, it does but it's not playable, as i mentioned on the original post.
Just checked the USA Custom's as you suggested and from the very few pictures I could find on a google search they seem to have the same type of heel joint as my RG560 where it starts full thickness at the top and gradually becomes deeper as it reaches the bottom, contrary to this body which has a deep cut from top to bottom. I'll leave those pictures here for reference.
Also the finish. From what I can see, those USA Custom's all have figured finishes while this one is just plain black (although it may look figured in the pictures, those are just cracks in the finish).
Lastly, I couldn't find any pictures of a USA Custom output jack so I can't confirm that one.

Could this be some odd model that got the Vai's heel joint cut and output jack placement?
Or maybe I'v been scammed with a fake body? Although it's a really good body and resonates like crazy while playing, way more than my 450 body.

Anyway here are the USA Custom pictures from google image search:
https://thumbs.worthpoint.com/zoom/i...c698da4f1f.jpg
https://www.12fret.com/wp-content/ga...1989C_back.jpg
https://www.vintagejapanguitars.com....Custom-pdf.png