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This unfortunately runs into one of the limitations of FairyGen: it assumes there are always at least two white pieces. It uses that for the application of symmetry to save memory: it only tabulates positions with the first piece in the triangle a1-d1-d4, and when it is on the diagonal a1-d4, with the second piece in a1-h1-h8. Other positions are mapped onto these by vertical, horizontal and diagonal flipping. But this is only done after white moves. The assumption was that a bare royal would never be able to win. Of course for 3-men EGT memory is not a very large concern, and even for 5-men the EGT would only measure 1GB (=64^5), which isn't much for today's memory technology. When I wrote FairyGen even my largest computer had only 1GB. I guess I could compile a version that doesn't apply any symetry at all, and try if that one does 1+2-men without problems. (I already have versions that I made for private use, that can handle reduced symmetry, like needed for the pieces of the CwDA Nutters army, but even there it still does horizontal flipping.)

To define divergent moves in the piecedef.ini file you can add an 'm' or a 'c' to the third parameter. E.g.

X: 1,0,sm* 1,1,sc*

would be a piece that moves like a Rook but captures like a Bishop. To define a piece that doesn't capture at all you just make all its moves 'move-only'. If you want a piece without any moves or captures, perhaps you can just leave the entire line after the colon empty. I never tried that, but I think it should work.