Thats is not correct, nobody closes their airspace for anyone, there still are the freedoms of the air. Also cabotage is allowed within the union so one member state can’t prohibit another member state airline to operate domestically within another country. Neither are there different entry requirements for each country within the union. The cluttered mess is mainly because a lot of populated areas are close together, not because of sovereignty. Eurocontrol has done a good job in making the upper information region one common Europe. Also Eurocontrol is implementing free route airspace, some countries already have it, others are in various stages of implementing it.