While I do think that Malva wasn't giving it 100% in that fight, Alan was still being portrayed to be close to E4 level since Malva still fought him a little seriously. His fight with a serious Siebold was to show his potential (Siebold admitted that even with a type disadvantage, Alan was able to corner them for part of the match) and that was still when Alan was relatively new.
Since then, Alan has thrown himself into every battle that he could (champion, primal legendaries, every mega trainer that he finds). The closing scene of Act 3 included him fighting a Mega Tyranitar for training so we can assume that he trained even more in the time that we didn't see. Also if we count the Mega previews, Alan has fought much more enemies and he has lost his fair share of battles and learned from them.
I think the strongest move of Malva's Houndoom based on its portrayal was Crunch. Crunch was strong enough to cancel out Dragon Claw. Dragon Claw was strong enough to sweep away Dark Pulse. Their Flamethrower was nearly equal. Taking that into account, once Malva saw Alan's Charizard was hurting from the Flamethrower exchange (it fought 9 battles and took a Crunch already), it ordered the use of its best move Crunch to finish it off. I think it's why she showed some surprise that Blast Burn had that much power to hurt Houndoom.
I'm of the opinion that if Alan was weak enough to be defeated by Malva who wasn't giving it 100% or if he failed against the first 9 fights, Lysandre would have just abandoned him and found someone stronger. I think the part where Malva didn't give it 100% was when she carelessly ordered the use of Crunch without knowing what Charizard's final move is. I think she expected it to be enough to defeat Alan's Charizard which was already damaged.
Crunch is a contact move, Blast Burn as it's shown destroys everything around the user so it can't be dodged up close which Mega Houndoom tried. If she was more careful and fought smarter using Flamethrower and Dark Pulse from afar, Blast Burn probably wouldn't have worked and Charizard would have lost an attrition battle since it was already tired and damaged.