The admin burden does not have to be that bad. The info on who and what to ask for each country is in Jeppesen and (sometimes) the internet.
The problem comes when the relevant authorities do not answer your request for permission ..... this can be solved (at a cost) by using a flight clearance agent who knows more people to ask and who's palm to grease.
On occasion I have simply gone anyway without permission and sorted it when I got there, one can get unstuck doing that of course.
It was easier in the days of the Empire though .....