I can't explain the registry, and honestly you're not supposed to muck in there. The SSMS tool reads the registry, but it may be reading a different place than you're looking and that would be the confusion. The reading in SSMS is what you should go on. there's probably a corresponding server property to this that you can read from T-SQL as well.

The databases don't have a security tab since they are dealing with users, not logins.