Not that I’m aware of.
Typically PPR and slots are arranged with handlers.
Not sure about overflight permits, as a UK operator we don’t require any in Europe, but I’m not sure about other countries. I’d be surprised if a normal CAT flight or private requires any in Europe no matter the country though (maybe a few exceptions!). You’ll have to check the AIP ENR for the respective countries.
If you find overflights are required, it’s much easier to use a 3rd party service to arrange these usually. JETEX are a good shout, but there are cheaper service providers