https://imgur.com/OqxWUmE
I have a suggestion try to exchange the location of aqua grunts plotting to mt. Pyre to Beauty Jessica. In short, Aqua scene first before Beauty Jessica battle.
I tried to triggered first the aqua scene before I battled Beauty Jessica and the game didn't bug and freeze.
https://imgur.com/j8HA9ib
But it's still okay if the cutscene will be sacrifice.
Well, the thing is it's not Beauty Jessica who causes this bug... It's those two Aqua Grunts. As long as they are on the screen or a few tiles away from it, any kind of battle (trainer or wild) will glitch out the game. For some reason when the battle ends, you stop controlling your player character and start controlling one of the Grunts. And also it has nothing to do with the cutscene itself, it's just if those two Grunts are there, the game will glitch out. Maybe I'll move the event as you suggested, so the Grunts dissapear before you can enter a battle close to them, we'll see.
And yeah, it is possible to trigger the cutscene without glitching the game out, but you have to be very-very lucky to not stumble into any battle.
Would Mega Flygon be here?
No, there are only official Pokémon and forms in the game, and Mega Flygon, sadly, does not officially exist.