You’re right, if projects have the same name, they can’t be under the same workspace.
But you can change workspace each time you want to change project.
When you launch SW4STM32, you can specify a new path for a new workspace (or File > Switch workspace), import the project A, and work ...
If you want to change and work on the project B, change workspace, specify a new path and import the project B.
note that you can work with several projects under the same workspace, but they must have a diffrente name.
I don’t undersant you 2d issue, can you explain more ?