Becoming professor and showing autonomy - when to exclude supervising professor from co-authorship Following common scenario:

You wrote a proposal for a larger several million € research project with several university partners after your PhD, the project got funded and you are the project manager, the professor is project leader and official applicant and principal investigator mainly visiting the regular meetings of the research alliance but not doing the micromanagement of employees, Phd students etc. He also encouraged the project leader to go for tenure, write a habilitation thesis etc. 

The problem I see: A researcher seeking tenure has to show autonomy, especially postdocs should leave their Phd supervisor for 1-2 years and join other research groups or industry before coming back to the old group and leading a subgroup. This is not written into stone, but advantageous facing a committee deciding professorship and many professors did go similar way.

In germany now the junior professorship exists with and without tenure after the professorship. But also the habilitation is still common to work for a professor. 

But how can you sell your autonomy? Should you negotiate hardly with your professor to publish some work on your own with him as a coauthor (who did neither conceive the experiments, in best case only review the publications internally before submission). Do you highlight you have to compete with junior professors later facing committees and need this autonomy in publications, also technically you are not the principal investigator, but do 95% of work to get money and conduct the project?

It's a delicate question to discuss this with your professor which you owe more or less for your PhD, but who also made profit from your work. Ethically, I know my professor has not many good reasons to be a co-author doing not much more then visiting meetings and reviewing the publications. Technically this is the common case, but due to junior professorships I think the situation changed a lot in comparision to 10 years ago when habilitation was the common and only way to become professor working until then for an already tenured professor.

EDIT: this is experimental sciences. So you are often dependent on expensive lab equipment of your supervising professor. Maybe an idea then is also to work more on theoretical papers, then authoring alone should be acceptable/negotiateable with professor?
Assuming that I understand it now, I do have a suggestion. Given the norms in your field, in which the PI is (I think) a co-author of every paper and who controls the grant and the research, you can't really distinguish yourself without help. But if others speak to your qualities more than you do, it might be enough - or even better. That would be the case in the US, anyway. Especially if that other is your PI and former advisor. You are, after all, his academic descendant. 

Suppose you are looking for a position elsewhere. Suppose your professor writes the letter that says you wrote the grant and were the lead investigator for much of what grew out of the grant. Not your words, but theirs. That is pretty strong. 

That may be easier to negotiate than trying to write as sole author, acknowledging the professor. Such might be possible, depending on personalities and norms, but maybe not. 

At the opposite extreme is excluding your professor unilaterally. I'm guessing that would be breaking norms in your field and place. It is also a terrible way to move forward if you become alienated from that professor. They are not going to be there for you either in career moves or research opportunities. 

In any case, it would be useful to have a conversation (or series of conversations) with your professor about this very question. "How can I distinguish myself here sufficiently so that I can move to an independent position? Can you help me do that? What should we do to enable it?" If the professor is honorable, and you don't suggest otherwise, you should get the help you need. And the professor, knowing the entire story may have options for you that none of us here can conceive of.