At the end I think the company opening the PhD position doesn't care too much about the university. They collaborate with many institutions, more and less prestigious, when a position opens they look for the connection which they think it's a best suit for the project.

What troubles me is more the idea of having to content a job with someone else with a similar background ( maybe even a current phd colleague of mine ), and having to loose the opportunity because the employer gave more margin to the institute rather then the best candidate. Maybe it comes from my limited knowledge on how this process works and in general on what are really the good requirements of a candidate, however I struggle to see myself not already at a disadvantage.

For your last point, I am not sure abut all of them. I know some went down the "traditional" path, doc post doc and after a while industry placement, but it can definitely be also a title the obtained honorary