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Well, one has to think ahead a little bit to keep the road to future extensions open, and not paint oneself into a corner. This is why I tackle a fairly large number of cases at once.

I don't see the unicity of the FEN strings as a serious problem; if the logic behind the various systems would allow a certain castling to be described in multiple ways, one can supply an additional rule to specify which method should be used preferentially. e.g. if K or H could be used to unambiguously specify king-side castling, one should use K. In the FEN reader I would not even pay attention to that, and have it understand both, as this is usually easier.

An important issue is how much effort one should put into upkeeping a unified approach, in which both game state and played variant are unambiguously specified by the FEN. One might wonder if it is sensible to require, say, that a position from Janus Chess and a position from Capablanca Chess should be considered as different positions from the same variant, 'fullchess'. This puts a lot of extra burdon on the FEN:

For indicating game state, the castling rights have to indicate only which pieces moved. Wanting the FEN to specify the castling method, or other aspects of the rules (e.g. if Pawns can promote to Chancellors, or not), might just be asking for trouble.

So perhaps I was overdoing it. It might be more useful to consider variants like Janus or Grotesque as distinct from Capablanca. KQkq could then be used to indicate castling rights in all three cases. Games with more than 2 Rooks could use the Shredder-FEN system without any problem, as long as there is only one King (so that all rights disappear once this King moves). Only in games with multiple Kings AND multiple Rooks there would be a problem.

This only leaves move notation. In particular in variants where a castling to a particular side can be performed in more than one way, like in Grotesque. A very general way to solve this in PGN would be to provide a mechanism to specify moves that displace more than one piece, by joining the moves with an &. So an alternative to write h-side castling in Grotesque could be Ke1-i1&Rj1-h1 (or in short, Ki1&Rh1).

In WinBoard protocol, the moves between engine and GUI are not transmitted in SAN, but simply as FROM and TO square appended to each other, with an optional 5th character to indicate promotion piece (e.g. e7e8q). Perhaps the best system there would be to encode variable castlings by using k or q as the 'promotion' character, to indicate if the K-side or Q-side Rook is to be used, and make the squares indicate the to-square of King and Rook, respectively. These notations would always be recognizable as not indicating promotions, as both the mentioned squares would be on the same rank.