You raise some valid points. I may look into doing a comparison chart--although the brief, completely unscientific research I did on this (before deciding whether or not to plunk down $50) showed Apple doing rather well.
From everything I have heard, iCal should be able to retain (at least) most of its functionality on any WebDAV resource. We'll have to wait until Jaguar is available to know for sure. Apple has really impressed me with its adherence to open standards as of late, and I think it would be in their best interest to keep them in mind when developing .Mac services and applications.
I don't see iDisk Utility working with other providers' WebDAV resources any time soon. It simply isn't configurable enough at this point in time to do that, and it wouldn't make sense for Apple to spend time making it so. If you're going with a third party they would probably have a Web interface for the same sort of functionality. And if you're providing WebDAV, you'll have your own configuration methods depending on the daemon used.