Yes, Joker is quite a bit stronger than micro-Max, and there is no reason why that should not carry over to Knightmate either. I had somewhat more trouble than I expected in converting it, though: initially I just swapped the pieces of code for generating the Knight and King moves, and the capture codes for the 0x88 attack test. I fixed this in 5 minutes, and this made it play fine aggainst itself. But it was rejecting perfectly legal moves from other opponents. At first I couldn't understand why.
But it turned out to be a problem in the way my move generator treats pinned pieces. It first detects them through the enemy slider list and own King position, and then hides them to the normal move generator, with some special code to generate moves along the pin ray. But a Knight in normal Chess never has any moves along the pin ray, while the Commoner in Knightmate always has moves along it. And it failed to generate those moves!

But I fixed that, and now it seems to play OK.
I have the feeling that Knightmate needs a quite different King safety, though. A normal Pawn shield just in front of the King is fine for Chess, as the King defends all Pawns. But the Royal Knight doesn't defend any of them, so this constellation is very vulnerable. It would be perhaps better to build a Pawn shield on the 2nd rank. On the other hand, King safety might not be as important as in Chess, as it is quite easy to evacuate the Royal Knight. In two moves it can jump from the king-side to the queen-side castling position.
About your WinBoard_F problems.
Indeed I have not implemented bitmaps for Commoner and Unicorn in all boardsizes yet (as, until now, Knightmate was a pretty exotic variant). So currently they work only in board sizes "middling" and "bulky". For other board sizes you would have to use font-based rendering (/renderPiecesWithFont="..."), where you could use George Tsavdiris' WinboardF font.
The default letters WinBoard_F uses for Commoner and Unicorn are M and U, respectively (in FEN and PGN). The existing engines seem to use N and K, however. (At least Dabbaba and Fairy-Max did, as in Fairy-Max the lpiece indicators are not yet programmable through the fmax.ini file, and are limited to the set PNKBRQEFWMACHG, i.e. no U. So I programmed Joker this way too.) So to use 'edit position' with the engines, you would need the additional argument to WinBoard_F:
/pieceToCharTable="P.BRQ...N.KYp.brq...n.ky"
to make sure WinBoard will use N for Commoner and K for Unicorn when communicating with the engine. Perhaps I should make this the default. Perhaps I should make it possible to set different default overrules for the two engines, as currently there would be no way to play two engine against each other that do not agree to the piece indicators. (If you want to use 'setboard' or 'edit', that is, or in rarer cases, to for under-promotion.)
Indeed the /variant and /pieceToCharTable are options that are not saved in the winboard.ini file. You have to give them on the command line each time you invoke WinBoard. (When playing with a tournament manager like PSWBTM, writing of the winboard.ini on exit is suppressed, and in that case all options do stick as long as you do not run winboard in the same folder by hand.) You could do that in the Windows shortcut, if you make one.