Well, they aren't necessarily on intercontinental flights. They are parked in safe houses next to airports, or something like that. The engine doesn't provide that level of detail, so one has to come up with an interpretation.
And, again, it is not necessary to do that. A good base network will cover you, mostly. Upgraded transports (pre-Skyraider) will boost that coverage. Savescumming will cover you completely (and don't try to tell me that's not how players deal with 'frustration'
). Lucky spawns will. And not every mission needs to be done, especially considering that taking out a Medium Scout in 1998 isn't exactly something non-hardcore players do, either.
I mean, we also have the 'military shot down UFO' missions as well. If non-hardcore players need a boost, you could up those. But I am categorically opposed to the philosophy that optimising your gameplay should not be rewarded or even punished. And that's what you're essentially arguing here.
Plus, ultimately, it's an issue of, well, immersion.
If the aliens were just dilly-dallying around their landing sites until the police/army/X-Com show up, how exactly do we still have a secret war pre-invasion?