I would like to draw attention to this, as I am sure TDE would be more widely accepted if more general standards were followed (however, I know the team is already working in this area)
The reason to avoid /usr/ is to prevent conflicts with KDE4. according the the fhs we are doing it correctly by using /opt/. While a lot of stuff is renamed, this solution is much more elegant than adding -trinity to all binaries or renaming every lib.
http://www.pathname.com/fhs/pub/fhs-2.3.html#OPTADDONAPPLICATIONSOFTWAREPACK...
Calvin