DenseBuds,
You probably can enhance the seal, but I think I'd try it the way it comes first and if it isn't a problem leave it alone but if it gives you problems, then start enhancing the seal. Also not all window AC units have the same quality of sealing between the two sides. Remember, a slight cold to hot air leak isn't a problem like a slight leak of strong odor filled air might be, so what is a good seal for their purposes may not be any where near good for your purpose. However, the leakage should be fairly minor.
Also if you are venting both intake and exhaust air through the same window, try to keep the hot exhaust air as high and far from the cool intake air as possible. You don't want to be pulling the hot exhaust air right back into the AC or your efficiency will go way down.
You would be surprised how much difference in the effectiveness of the unit can be improved some times just by creating shade for the unit rather than direct sunlight.
Great smoking.