I've done 8 pin, 9 pin, 21 - 9 pin and hard wire installs. I think it all comes down to what you have for space and what you are also including (speaker, Keep-Alive, etc.). Case in point, I've done 5 Rapido SW1200RS installs and for each one I had to toss the board.
While there is room length and width-wise in a Rapido SW1200RS for a LM-3S module (once you un-solder the inductors on the board), due to the angled roof top of an EMD SW, there isn't enough room height-wise for it to sit on top of the board. Hard-wiring also eliminated the extra wires on the 21-9 pin adapter. No idea if the new 21 pin module would make a difference in this install, but there's hope.
For a Bowser SD40-2, you need to sacrifice the space allocated to the speaker enclosure for a normal LM-3S and put a small sugar-cube style speaker under the stack. I suspect the new 21-pin module will drop right in and you can put a bigger speaker in the rear.