Honestly this doesn't really have that many spoilers for TWatWK, but it does have a few, so just to be on the safe side, I'm putting it here.
It is worth beginning this by noting that both the Water from the First Well and the Ancient Stones have healing properties in them, placed there by the Maker. The Ancient Stones are also called, “healing stones,” at least, I think they are. I'm almost positive I saw that in a footnote or in the books somewhere, but now I can't find it. I'm not imagining this, right?
Anyway....before what could be considered “The Fall of Aerwiar” occurred, the Maker and Dwayne and Gladys walked together (I think...), similar to Adam and Eve. There are two things that have been around since the beginning of time: one is the Ancient Stones and the other is the First Well/Water. We know that Dwanye gave the Water to other people, presumably to heal them physically, however we have no details regarding what was actually done with the Stones.
I am taking an educated guess, based on how the Stones work in the series, that someone, likely the Maker, used them to heal mind/heart and body of people in Aerwiar. This did not kill or weaken Him because…well, because He's the Maker. That's just how it works. While Dwanye could heal people physically with the Water, only the Maker could heal them spiritually (like how a person can evangelize, but only God can forgive sins).
After the whole thing with Will, the Well was more or less hidden from others when the Maker sealed it away and it could only be reached when He wants someone to reach it. It was quite similar with the Ancient Stones, where they could only be reached going through the specific Word/Form/Song ritual.
Now, Gnag took the holoré and the holoél, and he corrupted them. He used them for his own gain and twisted the hearts and bodies of people who truly did not deserve it. Because the Divine (that is, the Maker) was not involved in the melding process that, if completed by the Maker would be a healing process, it weakened/killed the one the life and spirit was being taken from (i.e. the animal/person 😬).
However, we know that the Ancient Stones can also be used for good. If the one who is melding with others has good intentions (truly good, Maker-centered intentions) it is both a melding and healing process. It heals those who have been afflicted in both mind and body, because the Maker's power, which rests partially in the Stones, is going into them, while also draining life from the one doing the meld because they are human and not eternal, nor all-powerful.
So, the point? Basically just my thoughts on the Stones and their origin intent and how they differ from the Water. I believe the Maker created them, placed His power in them, and used them as a physical way of redeeming others and symbolically accepting them as His child. Almost like an Aerwiaran equivalent of baptism*.
Is it a perfect analogy? No, because obviously the Stones are used in different ways throughout the series. But when the Maker specifically used them, I think this is what He used them as.
I'd love to hear your thoughts, because this is a fairly new theory I've come up with, the origin of it being the next WFS fic I'm writing. Also, feel free to call me out if I said anything noncanonical 😅 And this ended up being way longer than I originally planned 😅😂
*please, I'm not trying to start a war on people's different beliefs on baptism. Personally I believe that while people should be baptized if it is physically possible (because Jesus was baptized and we want to follow His example), they will not be condemned if they accept Him right before they die just because they didn't get baptized. God knows the heart. But baptism is very important, and if it can be done, I believe it should be.
I've heard Baptism as a portrayal of Christ's Death and Resurrection, and the stones could also be seen similarly to that. The main difference is that they can be used for good or evil, unlike Baptism.