Okay, I've figured out how Flight works! I made a test map, experimented, and now it's all clear. Later, I decided to check something else, and it was worth it. Pomazok1329 was absolutely right. I'm attaching my findings with screenshots. They will be useful for both players and mapmakers. So, flying over land works exactly as described in the game manual:

A hero can move through water and any objects on the adventure map, but cannot stop on them.

Another important, but not obvious, nuance: flying over land allows you to fly over any objects without interacting with them, BUT if you fly over a cell with an event, the event will trigger. Most likely, the same applies to the sea. The author of "Jedi story" even placed an ambush in one location on the sea that can only be bypassed with Fast Combat enabled; otherwise, the game will produce an error and crash.
And here's flying over water (surprise!) actually works almost the same as... walking on water: you can move from land to land only on empty water cells or cells with rocks. I tried to bend the trajectory in every possible way, and it clearly showed that it bypasses passage guardians, monsters, and border guardians, but ignores rocks.
Another interesting nuance was revealed here: the author of "007 chases Dr No" didn't randomly place these two water paths on the very edge of the map! The fact is that the standard map editor does not allow you to create a bridge-passage across an empty space less than 2 cells wide. The same applies to water: the minimum width of a channel is 2 cells. And only on the very edge of the map can you create a path or channel 1 cell wide. So, the author really thought everything through deeply.