I haven't experimented with Chess960, and I'm not actively writing chess engines right now.
But if I understand correctly, there isn't much difference between it and standard chess, just that the starting position and castling moves are different.

Perftree doesn't care about the specifics of how a move is performed, it doesn't do any position calculations itself. It just identifies a position by some starting FEN and a list of moves in UCI notation, and passes that information to the engines (your engine and Stockfish). Then the engines do all the position calculations.

So, if Stockfish can recognize the position as Chess960 and your perft script configures your engine for Chess960, then it should "just work". Or maybe Perftree just needs a small patch to configure Stockfish for Chess960 mode.

Chess 960 support #10

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