I generally fill mine to where you described. (The smallest diameter there below the fuel cap.) I cannot say I have ever noticed fuel odor and I usually fill the bike just before returning home. I have a station 3 miles from the house.
As for removing the charcoal canister, although I have taken it off all my other bikes in the past, I have had no reason to remove it from my Eldo. As long as everything is working properly, I won't mess with it.
In your case, maybe it was a fluke, or there is something going on. Considering it is brand new, my suggestion is to contact the dealer about it before trying a bunch of things yourself that might pose a warranty denial. After all, you do have a warranty.
John Henry