Doing some console rpm update/install one might see a "missing/failed dependency xxxxxxx" message.

Also, P.M.s using update rpms will flag up a dependency too.

However, this query is about when P.M.s say in their pop-up that "aaaa, bbbb, cccc will be removed" as well as saying what you expect to be updated/installed.

And of course, "aaaa,bbbb,cccc" are the latest versions and have nothing whatsoever to do with the package.

What's going on there? What is different that the P.M. wants to remove stuff - unrelated directly and fairly fundamental stuff - that won't happen with using console rpm?

Basically, although pkgs are in .rpm format, you wouldn't normally use the rpm cmd to update/install, as this doesn't handle dependencies.
Instead, use the yum cmd, which does.

It can sometimes happen that using yum to remove pkgs will cause a cascade effect in terms of dependency chains, so its always a good idea not to use the -y flag.
Instead, check what it says it will do and consider if its safe to confirm.
If not and you do want to remove stuff, then do use the rpm cmd, specifically 'rpm -e (or --erase) to remove individual pkgs.

http://linux.die.net/man/8/yum
http://linux.die.net/man/8/rpm