Is it safe or normal to close/cover junction boxes but use existing line to power new boxes just a few (6-12) inches away from the old ones?
There's no technical reason that he can't move the boxes. It would certainly be more elegant.

My best guess is that your electrician doesn't like drywall repair/ painting. If the ceiling is textured, that's a strong disincentive, as matching texture is hard. 

He'll definitely save you money with his approach.