I know of several fellow kayakers who use similar racks on their pop-tops to
carry kayaks.  Though they don't have the box you're talking about, the basic
rack is the same.  You buy 4 bracket-type things that essentially create mini
rain gutters like the standard van has, and you bolt them on to the sides of
the pop top.  Then you install the rack as normal.  I've heard that the pop
top will stay up and function quite well with 2 kayaks (80-90 pounds), but
not too much more.  Don't worry about the warranty.  Just buy the rack from
REI or LL Bean and you get a lifetime satisfaction guarantee.

Doug