Its an unfortunate outcome of the system. However due to how large the strategic air areas are (Two in all of france), you still will be intercepting planes on their way to their mission target. (a bomber heading for paris has to fly over a lot of land to get there!, and can be invalidated or shot down by fighters in that time)
Its definitely not perfect though. the british channel as it is, is useless. Unless you are fighting for direct naval supremacy and using your airforce to assist, there is no reason to protect the channel, or conversely fight to control it as germany. you just skip over it and fight in the skies over london.
I'd like to see expansions further down the track improve the system. i think its a great base system and it takes a lot of the PAINFUL micro out of the equation. Also, to be honest, it was pretty damn hard to intercept high tech aircraft in hoi3 for a player like me. They moved so fast and teleported around provinces that it was hard to spot them, let alone intercept them. This system is at least superior in that regard, where nothing will be sneaking in like that.
So the system has some unfortunate outcomes, but imo (just my opinion) its still far better than HOI3s system which was a real feat of micromanagement to play