I don't see why this is a problem, being able to farm stage 1 would only give Lv1 chests which would barely give anything worthwhile but enough for people who are stuck progressing to feel some kind of progression. If anything, you can just limit it to 1 chest or just a single card reward+coins per day/24hours from replayed stages and create some stamina system or something for the story, that way those stages don't become completely obsolete after you run them and give players something to do in-between waiting for their chests timers.
That sounds pretty awful and even worse when you look at the obtainable chest from winning 5 PvP matches, in which you either have to wait multiple hours to get by getting 5 separate chests one at a time or literally throw away 4~5 chests away while trying to get it immediately. Imagine if you got 5 12 hour chests from PvP, you'd have to wait nearly 3 days just to get the PvP chest without tossing away any potential high tier chests.About the chest unlock system:
There are lots of possibilities regarding a healthy unlocking system, all of them have pros and cons.
After you progress a little, you will find out that it's better for the player to actively choose what chest to open and when, depending on the time you have available for play.
Some of the implementations that create a better player experience also create vulnerabilities for the project so we have to be careful when addressing important (economy) issues, but we will think about methods for streaming up the process.
Chests have different opening times. On your 1st few levels you will get 15minutes, 30minutes chests ... but later you will get 1h, 4h ,8h and 12h chests (with different loot and, of course, chances of getting them). Also , keep in mind that the progress is getting slower as you advance and later you will find playing PvP more rewarding(talking about the number of received chests) then playing the sagamap.
Yea, I really don't see why you can't just have all of their timer start the second you get them. It's not like having it is going to stop cash players from spending any less when they can just outright buy the highest tier chests, it would only encourage players to play more and for longer periods, instead of just logging in to do a single match to get another chest and logging off. The locking system only acts as a wall for players who can't play the game 24/7 and is clearly deterring players from the game as you can see by the fact that multiple people have brought it up the matter.
Lol. I'd suggest you take a good look at what you wrote and what you're playing. There's even more irony with your post.