Hello! Updating from my side.
Thank you @SGaist for your answer, for future people facing the same issue: I did not have any uncommon character in the paths more than underscores.
My fix:
I figured with some help and testing deploying to other folder structures that qmake was the problem and complaining.
Placing the whole project one level up (C:\Repos\NewLevel\ ...) fixed the issue and no problem from Qt whatsoever.
It is purely a workaround that Qt seems to be ok with. As my version control begins after NewLevel, it is also not an issue. Maybe I will try in the future to take it down one level after some update in Qt, but AFAIK it is not a reported bug.
As I said, other machines with identical Project Strcture using same Qt Version and QtCreator seemed to be okay with that. The Makefiles look also the same in terms of relative paths.