I've just tested your scenario on several different versions dating back to 10.0.3, and so far I have not found any change in behavior in any version. They've pretty much all work the same. For testing, I started with a default config, and used CUA emulation with no changes. I created two seperate file trees with projects in one and source in the other, c:\projects, and w:\source and set the working directory for the project (Project > Project Properties... > Directories > Working Directory) to W:\source. Now, depending on how you got to Project Properties does change the behavior for the initial directory for Add Files/Add Tree:
(main menu) Project > Project Properties... > Files > Add File, the initial directory would be the current directory SlickEdit (cd on the cmdline). So if I was in c:\temp, the initial directory would be c:\temp.
(cmdline) project-edit, ditto.
(right-click on project in Project Tool window) Add Files... or Project Properties... > Add Files, the initial directory would be set to the project directory (the location of the vpj file).
The source for project-edit (macros\project.e; line 196-ish) command confirms that this is done deliberately, and it has worked that way pretty much since at least v7 from what I can tell, maybe earlier. I'm sure it was originally added on behalf of a feature request for people with multiple project files, but I'd have to go way back in the feature tracker to find when it was requested and why it was done that way.
Please double-check and confirm that your setup is working the same as I've described above. In none of the cases above was the current projects Working Directory ever used as the initial starting directory when adding files. As everyone has a different workflows and project hierarchies, no matter what we set the initial directory to in Add Files/Tree, someone is going to have a differing opinion on how it should work. I've spoken with both Clark and Scott about it, and we don't see it as bug as it's currently implemented. Now whether we should change the existing behavior, that is another story. If somebody makes a strong enough argument, we can consider making the appropriate changes.