Which are the best universities for a DPhil/PhD in proof theory and automated reasoning?
I'm aware of at least two perfect places.

Paris and suburbs. You might want to check websites of David Baelde/Gilles Dowek (ENS Paris-Saclay), Delia Kesner (IRIF), Dale Miller (INRIA Saclay).

Vienna. There is a strong group of Agata Ciabatoni and of Roman Kuznets.


You also might check the list of the accepted papers for LICS/CSL/MFCS/FOSSACS/ESOP/JELIA and see the authors of the papers that seem to be related to proof theory.