I know this, but GP was asking about how to do it with "different base directories" which I'm assuming is asking for an analogy to Subversion's multiple working copies (i.e. check out this location from the repository to this location on disk).
Yes you're right, the thing is, the project produces different binaries which should be accessible for all different versions, which was solved by having only different base directories, all the configuration files build to same subdirectories no matter which version. If I'd switch to "always having only one version in a single base directory" then I'd have to maintain different temporary output and binary output names in all the configuration files in every version which is quite ugly. Then I can't use any "known fixed subdirectory names" in the projects.