I recently did a Bowser SD40-2 with a 21 pin. Those Bowser SD40-2s do not have a lot of spare space!!
I couldn't get everything to fit in the install (LM, KA, Speaker, etc.), so I had to sacrifice the rear light as installed by Bowser. If memory serves, I also had to pull the light baffle for the class lights, but I can't recall at the moment (I'm at work and the unit is at home). If I get brave, I'll remount the SM LED for the rear light, but it's not a game changer for me.
The headlight and ditchlights work as supplied by Bowser. I haven't set-up anything else at this time, but I presume it should be workable. I'll pop the shell later this week and let you know.