In FDT 4, the settings for installed Flex SDKs, project templates and project types are stored directly in the user directory. This is the incorrect location for these files since this directory should be reserved for standard directories as defined by Apple, e.g. Desktop, Documents, Movies, Music, etc. If all applications stored support material in the top level user directory, it would rapidly become cluttered and unusable.
The correct location for these files is in the ~/Library/Application Support directory. This still achieves your stated goal: "We strongly believe that putting more and more settings to the user folder is the right way to go. It would put an end to setting up all FDT preferences whenever you create a new workspace."
Please see Apple's Developer Guidelines for further details: http://developer.apple.com/mac/library/documentation/MacOSX/Conceptual/BPFileSystem/Articles/WhereToPutFiles.html