I'm confused as well. But then i just accepted it because everyone was happy in the end.
I'm guessing:
Waki (the puppet Master ) created Kon as a "replacement" of Megane. He used him to satisfy his "needs". Meaning he can be used by all ppl who have kotodama, who can't use their own kami. Kon would do odd, dangerous jobs that the kotodama's didn't want their kamis to get hurt by. (ie. Every time kamis are used theyre torn up inside until their core expires.)
So when Raizou came into the picture, Waki just allowed Kon to go with him. (Meaning Kon still does odd jobs for ppl so he won't be considered "useless" and die)
But of course, Raizou is scared of Kon getting really hurt that he rushes Kon away. (Which is really funny)
Well, the rules were actually made by Waki right so they are not set in stone :) If you notice the instances where Waki imposed those rules strictly with Asari and others is when the Kamis were lost and kind of aimless. So he was using it to push them serve a new master so they can all benefit from the new bonding. However, he was ok with it as long as his Kamis were happy. He was worried that Kon will be sad so he was actually relived that Raizou is attached to Kon. I think Waki sort of sees the Kami (except Magane) like his children+best creation so he takes pleasure in both their own happiness and their capacity to evolve into real human beings.
Wait wait wait wait...all this bonding of kotodama and kamisama...how come kon became raizou kamisama? Raizou is normal human right? Not a kotodama??
Btw, still need to shout out that THIS IS THE BEST YAOI MANGA EVER!! Whoever feel reluctant to read please READ...although i dont hv fav pairing. I friggin LOVE them all.
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Except waki x megane...isnt they only like owner and his dog? And waki x rikiichi also cannot..rikiichi is seriously straight. He doesnt even take advantage of his kamis. Yeah, poor waki