I finally received my new Evoque 2 door and it's awesome.
I noticed that it had a soft but clear "crackle/rattle" in both doors. Because of the transmission of noises, it's always hard to clearly pinpoint them: for me anyway.
As I was going out of town, I left the car for 4 doors with the techs and they agreed. Apparently the 2 doors seem to manifest this more frequently. In any event, the guys tightened everything, placed insulating foam, adjusted hood strikers, lubed weatherstrips and adjusted gate stops. In other words, they applied "shotgun therapy" and it seems to have worked. Just the very occasional squeek.
Overall seems to be "multi factorial" and perhaps in the end it's just aggressive insulating that did the trick. Either way; it helped.
Good luck and safe driving.