Well, the first thing that comes to mind is that, in spite of what you read in lots of places, RPMs are not the only package format, and in fact they have quite a few problems. Don't forget .Debs, which would give us better access to Mac users (which I predict will rise in the next few years as geeks that want to do cool things with their computers, but want their computers to "just work" will discover the Unix inside MacOSX)...
But, you are right, if you heavily customize your OpenACS installation and install an RPM of the next version, it is a non-trivial (impossible?) problem for the package manager to avoid screwing up your changes, *especially* if they involve datamodel changes.
