I have struggled with this issue myself for a while and I think the reason it happens is because (for Android) there are two ways to import projects into the workspace
1) File>Import>General>Existing Project into Workspace
2) File>Import>Android>Existing Code into Workspace
The errors described here are related to method 2).
For method 1) there will be no overlap problems as long as you uncheck the "Copy Projects into Workspace" box if the project is already in the workspace.
Edit: There is a third method that wasn't in my original post.
3) File >New>Other>Android>Existing Android Project into Workspace