Some initial thoughts and ramblings.
This is a small tangent, but those who like to de-emphasize Mary sometimes claim the use of the word “woman” as a form of address as rude, as it would be in English. But that isn’t the case in all languages. In Japanese, for example, there are numerous honorifics. Older women are routinely referred to as “granny”, for example.
But that goes beyond your question. I suppose it’s a matter of circumstances. With the woman at the well, addressing her as “woman” isn’t necesssrily odd if we understand that it was not considered rude. He had only just met her. With Mary Magdalene at the tomb, at first he was concealing his identity, and Mary Magdalene would not have found being addressed as “woman” by a stranger/gardener odd. It’s when he calls her Mary that she recognizes him.
Mary at Cana seems a little different. It’s his mother. While perhaps not rude, the choice of the word woman seems underscored here.
But actually, I’m going to approach this from a different angle and claim all three women are written as types of Eve in this case.
The beginning of John is very specific. Six days pass, and on the seventh day there is a marriage at Cana. John parallels the opening to his Gospel with the creation narrative, in which on the seventh day there is a marriage between Adam and Eve. Jesus and Mary are obviously not marrying each other, but given the other parallels and this being on the seventh day, Mary as a type of Eve can be drawn out.
The woman at the well may also, in some respects, be a type of Eve. Isaac’s wife Rebecca was found by Abraham’s servant at a well. Jacob met Rachel at a well. Moses met Zipporah at a well. Wells are the places to meet future wives in the Holy Land! The use of woman here could very well have nuptial connotations, not for a literal marriage between Jesus and this woman, but between Jesus and the lost children of Israel or even the gentiles. The nuptial covenant will no longer just be between God and Israel, but between God (with Jesus as the Bridegroom (strongly emphasized in John’s Gospel)) and all peoples. (And if we go back to his mother, Mary, perhaps we can see instead an illusion to the covenant with Israel as Mary is a type of Israel/Daughter Zion in addition to the Church).
As for Mary Magdalene, I think there is an intended allusion to the Garden of Eden, emphasized by calling Mary Magdalene “woman”. She ‘mistook’ Jesus for the Gardener, which is itself a reference to Adam’s role in the Garden of Eden. Jesus is the Gardener, but not the one around the actual tomb, but on a grander scale as the new Adam.
Just some train of thought writing, but there is a lot of Genesis typology in this.