If the new CGI substitutions are just as good as the shot of the Enterprise approaching Saturn in BoBW then all is well, that looks as close to the original model work as they can get.
The stock shots in Season 4 I have a particular interest in seeing, I wonder if MV were supplied with the elements CBS-D use or did they have to composite them from scratch like HTV had to?
Oh certainly as good. When I visited CBS-D, I was shown several S5 fly-by shots which were thoroughly impressive only to be told afterwards that they're CG. They have done an amazing job in perfecting their CG.
I wouldn't have too many concerns about your last point. They seem to be far more "complete" in their shared elements, for instance the starbase shots from "Remember Me" (reproduced from "11001001") are just as beautiful, but with a nice bit of difference.