What we're really discussing here is what makes a watch original. What most auctions mean by "100% original" is that isn't a fake. By fake I mean a product made by one company as a product of another company.
With very old watches, it's not very common to find pieces that are "all original," especially since parts are hard to find for such models. For example, I have a 1957 Seamaster that's been redialled (very well, I might add) and has probably had a new crystal added at some point. My watchmaker installed a new crown that may or may not be exactly like the original was back in 1957. I don't really care because it works fine and is a genuine Omega part. It's also more than likely been through a few crystals and a dozen or so bands, and is currently using one that I bought at Wal-Mart. It looks good and functions quite well. As long as the case, crown, and dial are "correct" to the original concept and the piece is in good order mechanically, then it doesn't bother me at all if a little improvising had to be done. I do agree with you, though, that dials should not get custom paint jobs and hands--it just looks tacky.