I mean they could, but Cynthia is stronger in-universe (ranked 2 vs 7) and has more reputation among fans as a tough trainer. Ash could have beaten Alain last time they fought. Cynthia has mostly been portrayed as a cut above. Alain to Cynthia seems a more natural escalation.
I'm fine either way, as long as Ash wins both, but it'd be strange to do Cynthia first and then Alain second, since he's objectively a downgrade in ranking terms.
Also doing Alain in the SF and Leon in the final means we'd have two matches featuring Charizard as the ace in a row, which, idk, seems off to me.
The Master class rankings don't necessarily mean as much as you're making it out to be. By that logic, it makes no sense Ash is weaker than Iris when he beat her before, got to the Ultra Class first and also, never lost a single battle in the Ultra Class.
Plus, if you watch the Lance and Raihan battle against Leon, we don't really see much of a difference between the two despite Raihan being ranked 7 and Lance being ranked 2 against Leon. Essentially, it would be fair to assume everyone in the Master Class Tier are exceptionally Strong but one step below Leon.
As for battling two Charizard aces in a row, there is enough difference between MCX and Gigantamax charizard to create 2 different type of battles. Plus, Alain has the former MC Plot armor. They could very well, give him a win over someone like Steven (Who he fought previously in XY) and take him to the Semi-Finals.
The predictable route would be to have Ash fight Cynthia in the Semis. Having to fight her right in the first round, would up the stakes.
Plus, they can have Mega Lucario in the fight against Cynthia and then bring back its "Master of sorts", Ash Greninja for the Alain battle and then keep Pikachu for the Final Leon fight.
Personally, assuming it is a knockout, I would prefer Cynthia -> Steven -> Leon with Ash Greninja being used against Steven's Mega Metagross (After Steven defeats Alain in the first round). Would be a nice twist instead of the more obvious, Alain Round 1 -> Cynthia semi's route and we have a more interesting fight with Ash.