Let me first explain how you can automate testing with WinBoard. Unfortunately this is still a bit cumbersome, because WinBoard does not yet correctly handle engine-defined variants (like 'Apothecary') in matches starting from a set-up position. (Both the engine and the tournament manager try to set up a position then, and this seems to happen in the wrong order.) So you would have to do it the 'old' way, not relying on the engine to relay the variant definition to the GUI, but define the game to the GUI also by hand.

This would require you to make a settings file 'apothecary.ini' where you specify 'parent variant', pieceToCharTable, and initial setup. Something like:

/variant=elven
/pieceToCharTable="PNBRQW.A..C......GKpnbrqw.a..c......gk"
/testLegality=false
/loadPositionFile=start.fen

for apothecary1. You would then duplicate the apothecary1 game definition in the fmax.ini file, and change the name to 'elven', so the first line of the definition becomes:

Game: elven

(i.e. you also removed the stuf after (and including) the # signs. 'Elven Chess' is a standard variant in WinBoard (which Fairy-Max does not happen to play), so WinBoard does not expect Fairy-Max to send a game definition when it selects variant elven (as it would, because of the /variant=elven setting in apothecary.ini). You would have overruled the list of participating pieces (to correspond with Fairy-Max' own definition of 'elven', which really is apothecary1) with the /pieceToCharTable option, and WinBoard would not care how the pieces move (which is also different from Elven Chess) because you switched legality testing off.

The crux is in the /loadPositionFile. You would have to create the mentioned file, start.fen, too, and it could contain:

r2wccw2r/1anbqkbna1/pppppppppp/10/10/10/10/PPPPPPPPPP/1GNBQKBNG1/R2WCCW2R w - - 0 1
r2wccw2r/1gnbqkbng1/pppppppppp/10/10/10/10/PPPPPPPPPP/1ANBQKBNA1/R2WCCW2R w - - 0 1

These are two poitions for Griffins vs Aancas, one where white has the Griffins, one where black has them.

Now you are set up to start an automatic match. You start WinBoard with the 'Additional option' (in the startup dialog)

@apothecary.ini

which would make it read and obey the options in that file. It could be useful to register a 'clone' of Fairy-Max to WinBoard, i.e. load it again as second engine, but with a different 'Nickname', so that you can later easily see which one won the match. Anyway, once WinBoard is started with Fairy-Max both as first and second engine, you can go to the Options->Tournament dialog. There you specify the "File with starting positions" as start.fen, tick "Step through lines/positions in file", and Specify "Rewind after" as 2. Then you must set the "Gamesper match / pairing" to the number of games you want (like 100). You can also specify a file to save the games on. After that you 'OK' the dialog.

From the Mode menu you then select Machine Match, and the games will start. As you instructed, the first FEN in the file will be used for game 1, the second for game 2, and then the position file 'rewinds', so thatgame 3 is again played from the first FEN. Because WinBoard alternates the colors, the same engine will always havethe Griffins, and the result of the match directly reflects the Griffin-vs-Aanca score. You could also put more starting positions in the file (and increase the specified Rewind correspondingly), e.g. swapping Knights with Bishops for one or both sides, or swapping Champions with Wizards, to drive up game diversity.