Even in the version we have now, I've often noticed that Charizard can get knocked out of Flare Blitz by certain projectiles that it can usually armor through and it always happens after half the travel distance. I always just assumed that the super armor is only active 60-70% of the way after he starts flying. Basically I think it goes like this
1. Start-up where you have no super armor
2. The first 60-70% of the flight, you have super armor
3. 60%-95% OR 70-95% you have no super armor
4. 2% of the flight you only deal some pathetic 4% fire damage and pass through the enemy without falling down (there's a certain point where you just seem to pass through the enemy near the end of the flight)
5. The last 3% is Charizard finishing his flight so he doesn't damage the enemy and just passes through them
Looking at the video, I'm not sure about the distance because I'm used to the 3DS maps but I think that's about half of Flare Blitz's usual travel distance which is the point you can get knocked out of Flare Blitz. Later on, we see the super armor active when it collided with the aura sphere when it was definitely within 50% of Charizard's travel distance. Of course I can be wrong about the distance and they lowered the time you have super armor too which sucks.