That rack is mainly designed to hold one of the HighRock rack baskets with light loads, not really for supporting something long over top of the Jeep. Not sure how much your ski's weigh or what type of wind resistance you'll encounter, but you might try looking at a full rack if your budget has room. That particular rack only mounts via two bolts on each side--the holes in your tub for the hard top bolts. Also to work with your soft top you need to cut part of the plastic strips on each side of the top.
But I'm sure you could do it as long as you tie the skis down towards near the window as well.
Just probably not recommended.