Hi.
It actually wasn't uncommon for a matched kit to have a mixture of painted and un-painted interiors. I have seen them come up a few times over the years.
Answers:
(1) Because 1962-63 was right at that transition point where Ludwig started painting the interiors white and they probably already had some un-painted-interior bass drums made a little earlier, that they needed to get rid of. So, someone near the end of the factory assembly-line grabbed what was there and put a kit together and sent it out the door. Some drums were painted and some weren't. When the un-painted inventory was exhausted, then they all were white-painted. Most drumheads were opaque white in those days, too, so when the drums were all put together, there was no way to tell what the interiors looked like.
(2) More than likely, "yes". Sometimes pieces would have knots in them or voids and those would be puttied and then painted to cover the imperfections as well as giving a more uniform overall look. The 3-ply Ludwig drums were notorious for being laid up in different ways. For examples: The layup might be: mahogany/poplar/mahogany; They might be mahogany/poplar/maple; They might be maple/poplar/mahogany; They might be maple/poplar/maple. Don't ask me why -I have no idea! :) But, then later, in the late 60's-early 70's, the 3-ply shells were all made with a nice, clear maple interior ply that was finished in some kind of clear varnish. This may or may not have been related to the fact that drums of that era were beginning to become single-headed and interiors were exposed.
(3) Yes, the sealer would have a slight effect on the sound in that it would "harden" the interior surface and make it more reflective of the upper frequencies produced...but isn't really that perceptible...to my ears, anyway. Some say that it was used to prevent humidity from messing with the roundness of the shell...but I have old Leedy marching drums that are un-sealed and they were used to march outdoors -often in the rain. The outsides were varnished, but the interiors were "raw" so-to-speak. I don't think there was all that much "science" put into the idea as far as the sealer having an effect on the sound.