Can you check this info:

<<Google Reader is now working with one of my Google Apps for Your
Domain!! It's not working with my other GAFYD (the one I really want
it to work with). When I try to login with my other domain, I get a
login error that my password doesn't match my user name. I guess
Google is rolling it out to all GAFYD?>>
http://groups.google.com/group/google-reader-feedback/browse_thread/thread/b407a4fce251fdc6

If this is the only evidence, it wouldn't surprise me if that person had already got a Google Account setup which uses the same email address and password as their Google Apps login.

If not, how did they figure out where to login? None of the other Google Apps services share login pages with Google Account services.

A Reader Guide has just posted effectively the same as what Tony said.