While I can think of reasons why you operate with different license files for different projects, I still would be interested to learn what is your use case. My theory is you are a university user and when working on a project with a company, you want to make sure you don't use toolboxes your project partner doesn't have?
If my theory is correct, you may have a kind of startup script hat ensures you use the license file you want for the project. In the same script, you could add or remove directories from PATH. This way, you can work with one installation, but MATLAB doesen't find certain commands or blocks.
