One kayak shouldn't be a problem for a popup lift system. Two could be pushing it. I'm not familiar with the Outfitter's lift system but I think the one in mine is only rated to lift with about 150 lbs on the roof. Even with just 45 lbs of canoe on the roof, I can tell it's there. It's not bad though.
So, how much do the kayaks weigh? If I didn't have to offload to pop up, I'd do the roof. (And if I had to offload to pop up, I'd probably get inflatables because I'm done with trailers!)
On the other hand, if one never had to popup between home and boat-in-the-water destination, maybe it wouldn't matter.