If I am not mistaken, whilst there has been no official confirmation that William and Catherine will get Anmer, the popular view seems to be that they are getting Anmer soon. Allowing for renovations, I suspect a redecorated Anmer should be available to them within a year, which will serve as their retreat / country home. Their "principal" home in KP will be ready in the next few months. The rented home in Wales is in a very remote location, and time consuming to get to, so I agree, there is no need for them to continue with it.
I am not sure of the point you are trying to make. Clarence House is C&C's principal London home, whilst Highrove is their main country home, which is used most weeks.
The Duchy of Cornwall owns Highgrove, so as the Duke, Charles gets to use it. I have no idea whether he pays the Duchy any rent, but if he does, it seems silly, as the income comes back to him from the Duchy!
Birkhall, in Aberdeenshire, is owned by the Queen, and is only used a few times a year.