My R3T does not have the same filler cap as yours. I have taken the tank down to fumes a few times on long rides and do not sense a serious vacuum when I unscrew the cap. I did have an issue last summer when I over filled the tank causing a serious loss of power until I opened the tank after the first few miles. Once the guys identified that I was over filling it and I stopped topping it off, the issue went away.
As for the insects others have mentioned, I sure wouldn't rule that out. My bike is ridden just about daily and I often find some sort of bug under the cover in the morning from spiders to wasps and a few odd beetles. This time of year I look for them whenever I do my safety check; I’d hate to have a creepy crawler wiggle under clothing or get in my helmet during a ride. So having something clog a vent tube is surely not out of the question.