No. I don't tend to find it a problem in practice, things are just packaged to expect configuration after installation if needed rather than as part of the install itself. And it allows automated installs without risking having it stop because you missed a debconf question in the configuration. That's probably of limited relevance on a Maemo type system though; I can't see much of a use-case for kickstarting an N900 :-)
Yes. With a direct port of Debian's alternatives system.
Complex upgrades tend to work; I've done several Fedora major upgrades with yum. It's not strictly something Fedora support, but people generally try to make sure it works, and it usually does. I'm not sure exactly what you're thinking of when you say 'overrides' exactly though - if the dependency information is good and expresses the real dependency relationships between packages surely you want to use that information, not override it?