You're doing great at finding the optional stuff!
Although the quest doesn't tell you this, you can find the capacity upgrades in either order.
The second one will always be the larger, thanks to scripting shenanigans.
It should be noted that there's always an altar relatively close to each Crystalline Beast.
I've thought about making it where each one has an item requirement for facing them but never have bothered.
Anyways, that's 2 more down and another Crystalline Flame placed.
The mini-games are easy to access out of order, as you saw.
Each one is programmed with a clue telling you about the one before if you haven't done it yet or the one after if the current mini-game is complete.
Don't forget to go back for the stuff you can't do now later!
Every spot which has a panel marking it guards a secret which leads to stuff you'll want to do.