There is no problem with mixing platform packages, although it is not recommended. There are a few packages that do not have all of the possibilities (libqt4 seems to be one of them). I understand that i386 is being dropped because it is really redundant, but not all packages have been, or will be, changed.
There is a YUM plugin that will update wrongly installed packages (sounds like you got it done right), and there is a request for ANPM to support doing that, but it is not yet done.
You are right that any manually installed packages (ZIP, WarpIn, etc.), that are replaced by ANPM (RPM/YUM) should be removed to be sure that they do not interfere with the proper packages. Unfortunately, that is not always an easy task. The best approach seems to be to make sure that you install ALL of the packages that every program that you install (or already have installed) require, whether they are already installed, or not. It is pretty easy to install a new program that needs some package that you installed manually, but never updated. Then, some part of that program, that requires the later version, won't work. Trying to sort that out can take a LOT of your time, and it will probably take a LOT of, very valuable, developer time. Just do it right the first time, and everybody will benefit.