It is better to put the ski on two bunks versus a flat surface because if you look at the bottom.of your sxr you will notice that the lowest points of the ski in the rear are the intake grate bolts. they thread directly into the aluminum pump. by setting the ski on a flat surface you are basically putting a large amount of downward force on just two m6 socket head bolts threaded into soft aluminum.
I have not had any problems personally with the situation in have described, but I have talked to people who have (mostly during transport in the back of a truck bed with no bunks, one guy broke the pump where the intake grate bolts in).