It may be a niggly point, but did you account for the decreased volume of the driver inside the box? If you added 3/4" MDF to the front baffle, it's now 1 3/8" thick. The driver sits further out of the enclosure and occupies less volume in the box as a result. I'm guessing the difference probably means very little - but more knowledgeable people around here would be able to give a more educated opinion.
It's actually not a bad idea, IMHO, as it should provide more rigidity to the installation. Just as long as you have your volume calculations correct. That actually gives me an idea for my own in-ceiling speakers, as it's on my "to do list", to install backer boxes.
As for painting the boxes, was it vapour barrier paint? If not, it won't prevent air/moisture leakage. If your house is relatively young, I assume there is a vapour barrier between the ceiling and insulation. When you cut the holes in the ceiling, you pierced this barrier. If I were you, I'd wrap the boxes in plastic sheet vapour barrier and seal the edges with appropriate tape.