Chests can be found in pretty much all containers: I’ve found them dropped by skeletons, and in chests, pots, and baskets. I think also in crates.
So far as I can tell, you “unlock” runes as you progress. Alita will always sell you the one you’ve most recently unlocked. There are some findable runes in specific areas in the tutorial level, but you will have those runes dropping as loot fairly regularly through the game if you miss them.
Loot in containers appear to only EVER drop unlocked runes.
So assuming you buy them as soon as you can, your chances of finding an interesting rune in a chest are approximately nil.
And the facts that they are a fairly rare drop, and that you can’t even collect or sell them once you pick them up, makes it a slap in the face every time.
This is feedback we’ve given them heavily in testing, so I imagine they’re considering other approaches (including possibly just not making them drop!)