If you have the spare, I'd put it in, as the cap-hinge is under more strain being pushed upwards on it's pivot/hinge if the seal is in the wrong way. You have to push it down-sideways a little harder to close it, over time, it will get loose, and the hinge is not overly beefy as it is.
Probably not a do or die thing though. If you don't have the spare, I wouldn't worry as long as it isn't leaking, and its not being a pain to fill.
I didn't get the kit, but with mine, the one spare I did get was that seal. I think you'll notice a difference, and won't have to trim anything, and the seal will stay in place and not rotate, obstructing the fill port.
Why they didn't make them symmetrical, I don't know.
The other place I have heard of them leaking is the O ring on the coil base, both on the factory coils, and the RBAs. Mine is an older one, and apparently, the newer ones have crap O rings. I've never had a leak in mine.
http://vapingunderground.com/members/blacktoothgrin.19675/ did a remarkable bit of research, replacements are about $.08 apiece at a commercial O ring shop, and are made of Nitrile, whice seems much more heavy duty than the silicone. Here are the sizes:
1X9mm Will fit the dual RBA and factory coils
1X8mm Will fit the Clapton RBA and the chiminey O ring.
He was kind enough to send me some, they are black instead of transparent, and seem of much better quality, and apparently the factory ones I have are better than the ones they are coming out with now. These black ones are serious. lol