I digitized a lot of my albums and am really glad I did. And Vinyl Studio is definitely the way to do it.
Each track of each album has a filename/path tag associated with it. You can change that tag to a different filename/path to point to another version, but you probably have to do it manually. You may run into the problem that some of the tags, like album name, in the MC library may then be different from what is stored in the file. That should not be an issue in general but it is something to be aware of. Just be sure you do not copy tags to file or file tags to library.
Alternatively, you could copy the "good" version into the directory of each of the other albums. Again, you have to deal with the different tags in the library compared to in the files.
Personally, I would keep all the versions as they exist on the vinyls, unless there is one version that you think is clearly superior. It is just easier.