Have you tried putting the wheel in facing down? Makes it a pain to check the air but it should move the wheel center closer to the floor. I've had cars in the past where that was the only way to make the spare fit.
Yeah , I think that`s the way the manual shows it in there. While we`re on the spare tire/ jack subject, does the spring that holds tension on the jack (when in place) go around the lug wrench then to the jack or around the loop that`s welded to the trunk floor? The diagram on the trunk lid makes it look like it goes through the lug wrench????