I think this is an excellent game as is, although I am eager to see Mike's new piece sets. [Great to see you back, Mike!] This is also such an excellent game concept that's it's almost impossible to resist speculating about different pieces and piece sets; 'Alternate Pockets' can easily become as varied as Betza's Different Armies, in its own twisted way. And I suspect the 'Mutant Armies' can be at least as difficult to balance as the Different Armies. But I'm sure some of us can have fun trying.
On the nightrider vs rook question, what are the weaknesses of pocketing the opposing rook's pawn after a rook is pocketed and mutated to NN? This threatens RxP, then R-R8 on a following move. The rook is not a bad piece in PM, it pins pieces and projects power along a line very well. The nightrider has a different job, leaping around, forking pieces, and generally making a nuisance of itself. But, a player can do a pretty fair job of covering the back few rows against knight attacks well into midgame, no? If that's so, then the NN 'avantage' is gone from the early game. What's so overwhelming about the NN that it is necessary to change a rook to one?