I didn't find the soul coins in the ruins before the latest patch, although I may just have overlooked them. Anyway, I wondered whether their presence represented some sort of burial for the owners of the souls.
As for things being out of order, I believe some folks head straight for the grove instead of clearing the ruins first, so there may not be a "right" place to explain their value. I can't remember whether or not the first copy of the soul coin book was in the ruins.
Yes, Soul Coins were in the crypt before Patch 6.
I would bet that most people go through the crypt before hitting the grove. Sure, someone may do it in a different order, but when you're looking at the way things are structured, the most you can do is follow the most natural order. The crypt comes before the grove. So it's weird to get three Soul Coins, then get to the grove, get a fourth Soul Coin and suddenly make a roll to figure out what they are, as if this is the first time you've gotten one in the game.
It's clearly out of order. It feels "off," and I think that makes it worthwhile feedback.
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Not to mention the confusion issue that comes up with Raphael, which is also worth mentioning as feedback. The correlation between getting the Soul Coin and then the devil showing up probably didn't feel so obvious in development as it does during play.