At the time I wrote that there was a problem with engine-defined variants running in a match that started from an externally set-up position, where the position sent by the engine overruled the position requested by the user. But I think this was fixed in the latest beta version of WinBoard. There it should be possible to run a tournament or match specifying a 'position file' in the Tournament Options dialog, which contains the FEN(s) of the desired start position(s). I hope.
At the time I wrote that there was a problem with engine-defined variants running in a match that started from an externally set-up position, where the position sent by the engine overruled the position requested by the user. But I think this was fixed in the latest beta version of WinBoard. There it should be possible to run a tournament or match specifying a 'position file' in the Tournament Options dialog, which contains the FEN(s) of the desired start position(s). I hope.