It has been a super long time since I looked up the background of AIR, but I’ll see what I can remember.
The idea of AIR, and this is obvious, is that reincarnation is a thing. Not only that, but reincarnation doesn’t work hand-in-hand with the concept of time. Misuzu is one of many reincarnations, as is Yukito and every other character. The other reincarnations can exist in the past, in the future, and in the present. There’s nothing stopping the same “soul” from existing within two people at the same time. I believe there was a specific religious belief that went in line with this, but I don’t remember.
Yukito isn’t the direct son of any of Kanna’s companions. He is a long descendant, hence why his magical powers have faded so much. The magical bloodline of which he descends from has been diluted by the constant mixing of normal human dna. One of Yukito’s ancestors gave birth to a normal human’s child, so did the next one, and so did the next one. Yukito’s mother was just his mother. Dunno why that’s a question, but yeah, his mother taught Yukito about his ancestors’ traditions.
AIR is ultimately a small part of a larger story. These characters are effectively meaningless to the grand scheme of things, but it is the only link of an endless chain that we know about.