Okay guys, I figured out the final two routes. Credit goes to OnceFallen for finding the first route, on Glacier. Desert and Sea were located by me. Here they all are. This'll net you both hidden trophies.
Easiest way to get these is to use what is essentially the free flight mode:
1) Go into multiplayer
2) Create a game
3) Select any gametype, set it to unranked, 4 players max, and 3 private slots
4) Select the stage you want to play on and begin the game. The time of day doesn't matter.
HIDDEN FLIGHT RUN #1
There are actually two routes here and either or both will count for completion. In the western face of the mountain in the far northwest of Glacier you'll see a gaping ice cave high up. Fly into this cave, through the mountain, and emerge on the other side for the trophy. There's a second ice cave entrance immediately after this one that follows a longer path through the mountain range and will deposit you at the southern end of Glacier. Either of these paths individually counts as completing the Glacier run and will activate the trophy, but you might as well do both just to be safe.
HIDDEN FLIGHT RUN #2
At the southwestern edge of the S-shaped canyon running through Desert there is an arch bridge across the canyon. Fly above the road but below the arch, going across the length of the bridge.
HIDDEN FLIGHT RUN #3
Start by going to the northwestern corner of Sea. To the east of you you'll see five oil rigs. We'll number them in order from west to east, Oilrig 1, 2, 3, 4, and 5. For this run, ignore oilrigs #3 and #5 (the southernmost central one, and the easternmost one). You'll want to come at Oilrig 1 from the west, fly under its supports, and then fly the most level, straight line you can through the supports of Oilrigs 1, 2, and 4. You won't be able to do a completely straight line as these three rigs aren't perfectly aligned, but just keep it as straight as you can. Try and maintain a stable altitude, and to adjust directions, use your rudder (L1 and R1). Also, this run seems to be speed dependent unlike the other two, so make sure you fly it as fast as you can manage. This route can also be done in reverse.
If you're having trouble, the following diagram should help.
You're Dangerous (Bronze)
Complete any one of three hidden flight runs.
That’s Right, I am Dangerous (Silver)
Complete all 3 of the hidden runs.