I'm testing with IE11 and I have created an entry in my Site List using the Enterprise Mode Site List Manager for a top-level domain to render as default and then any sub-domains to render as IE9.
For example:
In the "Add new website" dialog in Enterprise Mode Site List Manager, the "Launch in" section would list "me.contoso.com" as "Default Mode" and "/*" as "IE9 Document Mode".
The problem I'm seeing is that each time I navigate to any of the me.contoso.com/* websites, those sub-domain sites all render the same as the top-level domain instead of in IE9 Document Mode.
I've tried several combinations and the only thing that seems to make any of my "/*" sites render in IE9 Document Mode is to set "me.contoso.com" to IE9 Document Mode.