Hi Kevin,
I am one of Davids colleagues working on this issue and I thought I'd give you a bit more background.
We have a Google Apps for Business account with approx 75 domains already manually added and verified in the dashboard under Domain settings > Domain names. This is to support users that we are on-boarding from legacy email systems where the users need to have email addresses at multiple email domains. Manually adding these domains has become quite an overhead for us and with another 380 to register in the near future I'm sure you can understand why we'd like to use the API to try to automate the process in one hit.
In answer to your question, we have never used Webmaster Central but I've just logged into it for our production system (the one with 75 domains) and I can see 27 verified and 6 unverified domains (far less than we see in the Google Apps control panel).
When I login to Webmaster Central for the test domain that we have been running the API against I see the domain that we registered via the API showing as verified but this is not mirrored in the Google Apps control panel and the domain is not available to the Google Apps instance to assign email addresses to users.
I'm hoping you can shed some light on whats happening here, why there is a disconnect between Webmaster Central and the Google Apps control panel and what we can do to leverage the API to get these 380 domains registered without doing each one manually (and probably losing my mind in the process!).
Thanks
Gary