I've got a 2016 Road King configured as a solo bike only. No passenger seat or pillion, so I took off the passenger floorboards. Does H-D or any aftermarket companies make anything that covers up and/or plugs the mounting holes?

 

Black Plastic plugs available at any hardware or a dab of black silicone will do the trick

 

This.

I've done black silicone for a few customers, and it works quite well, and its cheap.

 

I put polished button head screws in all the holes.