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'If the effort isn't too big' is a big if. Normal chess, Capablanca, FRC and CRC are similar enough not to cause too much trouble. Although I consider it already a nasty trait that some of the rules have to be implied by the board size, such as to which pieces a Pawn may promote. If a board width of 10 is taken to imply Chancellor and Archbishop are allowed, the problems with Janus Chess or Chancellor Chess I would consider already pretty bad. To unify those with Capablanca/CRC would require different letters for their Pawns. In Janus Chess you would have to indicate the deviating castling mode amongst the rights.

In the O-i-h system you would always be able to deduce if the K-side or Q-side rook is to be used by the ordering of the King and Rook destination? I guess we could indeed consider it a defining property of a castling that it swaps the order of King and Rook. I am not aware of any exceptions to this, even in FRC/CRC the King is required to be between the two Rooks. So I guess your system is acceptable for in the PGN, with the additional preference rule that if there is only one castling possible to the given side, it would be written as O-O or O-O-O.

The way the move is transmitted between engine and GUI in WB protocol is a matter specific to the WinBoard GUI. And WinBoard does generate the list of allowed moves itself, there is no way in WB protocol to request it from the engine. As this type of castling with multiple King and Rook destinations is about as crazy as they get, anticipating this format would probably enough to cover everything. Even the normal castling requires the GUI to recognize castlings, and know which Rook to move and where. (This caused problems when I had Fairy-Max play Cylinder Chess, as a King crossing the side edge was considered a castling, and led to the displacement of a second piece on the display board!) In fact, with the assumption that the relative orientation of King and Rook destination squares implies which Rook has to be used (and even if there are several Rooks on that side, only the one nearest to the King could be involved in castling), there is no need to convey any information in the 5th character other than that it is a castling. So an O here would be quite convenient, as promotion pieces have to be lower case in WB protocol.

For a really dumb interface (like my battle-of-the-Goth javascript viewer) it is necessary to fully specify from- and to-square of each piece that is moved separately. So there I transmit O-O as e1g1h1f1 and e4xf5 e.p. as e4f5e4f4.