Well, it's quite simple. Sevii Islands were FRLG's aftergame, it's own unique thing, but you're okay with putting them in ORAS' aftergame. So by the same logic, is there any problem with putting DPPt's aftergame of Battle, Survival and Resort Areas in BW's aftergame?
Sinnoh's after game was a part of Sinnoh already; it just wasn't accessible until after you'd completed a certain qualification. That's happened in every game, from Route 111 in Hoenn's inaccessibility until after earning the Dynamo Badge to Sunnyshore's inaccessibility until completing the Spear Pillar/Distortion World storyline. The difference is that the Sevii Islands could actually be counted as a separate region, parts of which were already accessible from Hoenn in Emerald.
All of the qualifications to include them are present; Mr. Briney's Ship, precedence (albeit through events), and the uncertainty of the remakes of the Kanto games. It certainly isn't impossible, just a bit improbable; it's something I would like to see, though. As it is, I would not be surprised to see the inclusion of Navel and Birth Islands as events, even if the Sevii Islands aren't included.
Not necessarily. Is the distance between Hoenn and these islands ever stated?
I think it's also pretty clearly obvious that they never done this for any story reason; it was just so people with the newer game could get the events to the awesome legendaries FRLG had.
Was the distance from Kanto to the Islands ever mentioned? I don't really see what their distance from Hoenn has to do with anything, given that Hoenn, Kanto, and the Sevii Islands are all based out of Japan, and they are already interconnected... Even if it was to allow Emerald access to certain legendaries, the connection was still established.