overcoming the scene tracker

I could see that as an option, but I don't know if it's strictly mechanically "fair."

If your Scene includes a Challenge element, and the Challenge requires 4 Overcomes to beat before the end of the scene, but also they could Overcome to add a whole extra turn to the Scene, then the economy of actions is kind of spoiled. In other words, I think delaying the Scene Tracker would be a more economical use of an Overcome action than actually addressing the Challenge.

Also, I think that might result in Cleric Syndrome (that thing where the Cleric has to spend all their turns healing and it turns into a very boring thing for the player).

I also find in my experience running the game so far (I've done 3 sessions with 4 total scenes) that running off the edge of the Scene Tracker isn't a big risk. The PCs kind of enjoy hitting Yellow so they get some of their cooler abilities. Then, when they hit Red, those Red Abilities really tend to unleash absolute destruction on any baddies left in the scene. In 4 scenes, only once have we gotten to the first Red space of the Scene Tracker.

Now, I've been using the standard Scene Tracker. If you want a longer scene, I'd say just add spaces to the Scene Tracker.

The other thing I'd suggest is more dramatic in game terms is - instead of an Overcome to stop the Scene Tracker - add a threat (maybe via a Twist) that requires an Overcome action, and tell the PCs that if they don't Overcome the threat before the end of the next turn, the Scene Tracker advances (without the Environment taking a turn, I'd say). You can even add an extra space to the Scene Tracker with this in mind.

Anyway, this is all from the perspective of a GM, so... there's that!

And, if the end of the Scene Tracker means something bad for the players, then I think the Villain getting to push the Scene Tracker makes sense, since they are generally going to be outnumbered by heroes. You can always take rules to some ad absurdum case, like, "Well, if 4 heroes face 4 villains and each villain Overcomes to advance the Scene Tracker, then they can end the Scene in two turns!" And, yeah, a GM can do that, but uh... they shouldn't.

I generally allow my players to make Overcome actions to untick boxes from the scene tracker, but there is emphasis that doing so makes you look more dangerous to the villains and environment. Oh, you spent your turn without anything to really do unticking a box on the scene tracker? Turns out that a second Blade Battalion just came around the corner, and they're now converging on you.

In general, I find that Twists tend to be both an incentive to players to make Overcomes, and a deterent against making them needlessly.