SOME 6.5"s will fit flush with no modifications. Some will require some trimming of the stock hole, or an adpater ring can be made out of MDF to allow the space for it to fit.
I would personally just go with 5.25"s in the dash and soundbar to have balanced sound. You may notice a slight improvement in bass with a 6.5", but it is negligable at best. I personally go for the matched sound over the larger coaxial. A sub is your only solution to bass worth fighting for. Coaxials were never designed to reproduce super low frequencies; pick a coaxial that shines in the higher frequencies.