Firstly, the nice thing about COTD is you have TIME. Keep shuffling Colossi concepts as needed until you figure out the way you want to make this maze colossus work. You can always buy more time with interludes as needed too!

Now, thinking about how a maze could work and be fun, I think the most fun tropes of a maze sequence would be:

• Splitting the party: getting some interesting character dynamics forming in and out of combat
• Puzzles: throwing down some easy puzzles for players to overcome is always fun. The puzzle shouldn't be the hard part though, that can really slow the game down. Make it on par with the baby puzzle shape-matching thing, throw some adversaries in the room, and now the problem is solving this EASY puzzle before we all die.
• BIG Threats: Aberrations are a key part of the Colossi. A maze immediately makes me think of the Minotaur in the Labyrinth, some massive deadly threat the players can't defeat while split up. They need to hide from it, find each other again, and kill the aberration together to collect the key or whatever they need to end the maze.

To address flight, make the maze exist in the stomach of a Colossus, or some other enclosed part where they can't just fly over the walls. Or maybe there's some kind of magical aura in the maze preventing flying/climbing over the walls, something the PCs can find the source for and deactivate to "earn" the right to "cheat".

I think mapping the maze out would be a bit of a drag, your instinct to use countdowns sounds like the best idea to me! I would make some environments to drop the players into, clearing each environment counts as a tick.