"Client created domains end up in clients/client0/webX yet symlinks are created to them in clients/clientY."
Yup. there is a bug here. It seems that I have found if the admin creates a website for a client, then the website is not added to the client's folder, but rather to the admin's folder.
I think that the problem lies when the site is created and how the clients id is retrieved. But after looking at file interface/web/sites/web_domain_edit.php I think this could be a feature rather than a bug. It's worth asking Till about.