We moved from requiring to get a single S on a champion a week to get a chest, to requiring 5+ games on a champ for a chest.
Added to this, you no longer need to be top-performing with a S rank, means I see no reason why you shouldn't be allowed to get progress on it in Arena.
Considering they want to see whether or not this could be a permanent gamemode...why not treat it as such, even Aram can grant you progress on the mastery despite being an absolute chaos festival; why can't Arena?
Just make it so you need to be at least 5th place or smth for a "C" equivalent ranking.
I by now only play arena, day for day, n I know many people do the same, so it's essentially forcing us to play an extra 2-4 hours of a game mode I do not enjoy anymore, just t get mastery and a chest?
Before the change, I'd just pump half an hour into a game, get my S n call it a day, that is no longer possible.
Edit:
Link to Riot'er response, this will change at some point!