How to sort issues over authorship in my manuscript with PhD supervisor?
It's unethical to include the name of a collaborator who contributed nothing to a particular paper as a co-author. However, as you said, it can be difficult to confront your advisor about including someone else as a co-author. 

If you are the person responsible for submitting the manuscript to the journal, one alternative you might have available is to ask your advisor is to have an explicit assignment of duties in the cover letter for your paper. ("Author A did activities Q, R, and S, while author B did T and U, etc.") The tasks of each author would be provided in such a manner—and in principle it would be hard to justify the inclusion of someone unqualified to be a co-author when you have to "certify" it to the journal, rather than just providing a generic statement of authorship.

If the advisor is unwilling to come up with such statements, then you could make the argument that since it's typically a requirement of journal submissions nowadays, that you're uncomfortable including an author whose contributions can't be clearly delineated.