If you don't want to hear the clunk, try engaging the clutch and backing the bike up a few feet to break the clutch plates loose. Usually works on my Harley and GSA.
Doing that before you first start it is one thing, doing it at every stop sign is another. I don't know if it is clutch plates dragging or oil flying around or something else that keeps the mainshaft turning in neutral. It is annoying and I cannot believe that it is harmless to the transmission. I will be shopping for an extended warranty on this bike.
My 18 GSA clunks and lurches when I engage first gear and the dealer claims that this is normal! Interestingly it doesn't do it when the bike is cold. This is the fourth GSA I've owned, the previous three had dry clutches, and in my humble opinion the clutch operation on my Rallye is far inferior to the older bikes.