Supporting the upstream is different. One cannot simply download AOSP and install it on your phone, however custom roms provide something you can actually download and install. Google deliberately does not improve the AOSP base applications because they don't want people using their proprietary apps. Google mainly supports AOSP because they can get more people hooked on google services with it than they loose from things like Kindle.
So directly supporting an easy, installable downstream with bells-and-whistles like cyanogenmod would be a serious threat to google.
With a little bit of careful adjustment to settings, you can disable all Google services on a Nexus device. It takes a little effort, but it can be done - unrooted and unmodified.
interesting. I'm aware that to quell anticompetitive accusations, google allows removal of many google apps and disabling of many services. But I believe the Google Play Services is deeply embedded in the google stock rom such that it can't be safely disabled in entirety.
The same argument applies to AOSP (cyanogenmod's upstream), but that hasn't stopped Google from supporting it.