On a test mdfind does still seem to pick up the system contents.
Possibly this is the kind of behaviour Apple was expecting ... I do find it odd that they didn't give an option for you to include the system searches by default, but I'm betting a bit of digging will lead to a plist change that will do this.
Yeah as soon as I saw that spotlight didn't do it by default I checked mdfind. However i usually use Property List editor to mod them it isn't that convient to use mdfind.
I actually did a bit of digging around and couldn't find it.