"1. You cant make smart collections that search multiple events
2. If you 'Favorite' parts of a clip for one project you have to unfavorite the clip to 'Favorite mark' an overriding segment of a clip used in another project."
Actually, no, I've not seen any way to create a Smart Collection that searches more than one Event at a time. You get an error message the operation could not be completed.
Yes, Favorite ranges (be is the whole clip or a section) can not overlap, but will combine to be one range. Keyword ranges can overlap.
This is all based on Final Cut Server (same database engine that is native to Mountain Lion, in fact). When you archive, think about going into the Project Library, select a Project, Duplicate it, and specify your Archive Drive, and include Only Used Media. That way you can retrieve an archived Project in it's entirety at any time. Once archived, you can delete that Project.
Just throwing that out there.