How do Pilots Actually Setup a Flight Plan?

Must have been long time ago, I’m flying primarily in EU airspace and I have never had such issues. It happens every once in a while that you would need to reroute due to military exercises but not 8 times. Especially in upper airspace that wouldn’t happen nowadays.

I’m not sure why you need overflying permit, that is a freedom of the air, unless you were transporting weapons of war or fly a state aircraft should not be required. Nothing is free for anyone, also not for EU registered aircraft.