I'm comparing rims with 40mm and 38mm offsets. Question is will the 2mm difference really show in the rear when measuring how close it is to the fender...or is the difference too small to tell?

if we are talking about some wide wheels, like 9 and 9.5" yes the 2mm would make some difference but in your case (I think 7.5" wheels) no not really but it is always better to get the lower offset, Sean