Chess960 vs. Chess480 castling moves? Which is better? In the chess variants Chess960 (aka Fischer Random Chess) and Chess480 the castling moves are radically different. 

Do the castling rules in Chess960 favor established FIDE Chess players more than the castling rules in Chess480 and if so why?

What are other reasons to favor one castling system over the other?
I believe the premise of the question is rather unclear! If you're already saying that there are a set of FIDE rules for castling, then the comparison between other types of chess should be straightforward, wouldn't you say? Either they follow the rules or they don't, whereas you seem to be asking for a crude-subjective-qualitative comparison here (you use words like "which is better" or "favored"...), which is kinda impossible because castling in standard chess has well defined rules.

First off, unlike the well-known chess960 mode, chess480 still lacks a coherent definition as many different types of it exists apparently(one where queen has to be restricted to appear on the left of the king, other where the king has to be on dark squares etc.) so as long as there's not a coherent and consistent description of the game, it remains very difficult to do any comparison (unless e.g. you ask for a specific scenario).

But anyway, all that differs, is basically the positions of rook/king after castling, in chess480 in certain scenarios, if possible, unlike Chess960, the final position after castling will not be the same as the final position of a castling move in traditional chess. Quote and image from Wikipedia:


  the king is transferred from its original square two squares towards
  (or over) the rook, then that rook is transferred to the square the
  king has just crossed (if it is not already there). If the king and
  rook are adjacent in a corner and the king cannot move two spaces over
  the rook, then the king and rook exchange squares.


In chess480: 



In chess960:



So as far as traditional castling rules are concerned, they are both equally undermining, as for one thing in either mode, the kings can be found on squares other than e-square in the initial setup and still be castled...

Maybe you could further clarify, as to what exactly you intend to achieve with such comparison. (and if you do, then I will edit my reply accordingly.)