I don't think the wiper motor would need to be removed. On the stock wiper area, they are recessed quite low in the cowl area. There are depression in the cowl where the wipers reside. The new one is flush fitting, so it should be well above the motors and the little nub the wipers get bolted onto.
I believe this is the reason the OP states that it's a two-piece design, for those with strict inspection requirements. Allows you to quickly remove the carbon fiber part, and put the stock items back on to pass the damn inspection requirements. Fortunately, I don't have to do either that or emissions.