Electric Motorcycles

Motorcycles are not considered in the parking credits, so EV charging for motorcycles would not count.

I realize this is probably because the credit reflects the US market where motorcycles (especially electric ones) are a much smaller share of vehicles than in some other countries. If you can show that you expect a high percentage of motorcycle commuters/visitors, you might ask USGBC for an exception. 

Does the Reference guide state that motorcycles are not considered in the parking credits?

I am not able to find any reference to motorcycles in LTc8: Green vehicles

If the parking spaces closest to the main entrance are for motorcycles is that a problem from the point of view of the preferred parking?

This info is found within the Overview section of Location and Transportation page #56 "motorbike or bicycle spaces" should not be included within the total parking capacity. 

The LEED reference guide states that "include motorcycle parking as vehicle parking space" within the Heat Island Reduction step-by-step guidance section. However this language was reversed per Reference Guide Correction 100002212. https://www.usgbc.org/leedaddenda/100002212