If boss is my PhD supervisor, is a wage negotiation inadequate?
Your post has the unusual feature that part of your first question actually answers your second question. Namely, you write:


  However, I want to avoid that he cancels the offer due to inadequate behavior from my side.


and then ask


  Comments about if the constellation boss=supervisor is problematic are also welcome!


Well, yes, it's indeed quite problematic, and that is precisely related to your worry about your boss/supervisor rescinding the offer. What's got you worried is that there is a huge, glaring conflict of interest here: one person is making decisions that two separate people should be making on behalf of two separate entities with very different interests. There might be some rare individuals who have the ability to separate their different interests and act objectively and without malice in a situation like this, but I fear that the mere fact this person has put himself in such a conflicted position already does not send out a very reassuring signal about his common sense and good judgment. Consider this: if I were in a similar situation and through some unlikely turn of events ended up as a dual boss/supervisor looking to employ and supervise the same person (something I'd be already very wary of doing and try my best to avoid), the first thing I would do is to bend over backwards to reassure my student/employee that I am taking every step imaginable to separate or manage my conflicted interests, for example by emphasizing repeatedly and vocally that the discussion of the student/employee's salary in the commercial employment will have no effect whatsoever on their graduate school funding or supervision, or by having the salary negotiation be done by a different person in my company, or taking various other measures to alleviate any concerns the prospective student/employee might have. From your question it sure doesn't sound like he has given you any such reassurances, which suggests he doesn't consider anything about the situation to be problematic -- not a good sign.

Now, I'm not saying such hybrid PhD/commercial employment arrangements never happen or cannot be made to work. Maybe his intentions are completely noble, and maybe in Germany there are cultural norms that make such behavior acceptable. But based on the details you've provided, and from my (U.S.-centric) point of view, this situation raises some serious red flags. Honestly, this whole arrangement doesn't sound like a good idea, which makes the question about salary negotiation a bit moot in my opinion. Before starting to talk about salary, I'd want to have a good long discussion with the prospective boss/supervisor about the viability of the arrangement, including discussing specific details about how you can make sure that he will not be incentivized to abuse his dual position of authority over you.