I believe that certifying a product can run in 2005 only in compatability mode is so companies can move forward with upgrades. Some products will not run in 2005 because of the changes in the way 2005 did security among other things. In compatability mode SQL server still functions in the same manner. Some vendors have not changed their applications to function properly in 2005 mode. I would find out what the vendor is planning when 2008 is released.