The flat racks have two major advantages, first is modular. With the T-Nuts, you can add sides, add tiedowns, add diffrent carriers and mix/match any combo. The second is low profile. Looking at the sight, it appears theirs is designed to go on top of your factory load bars. Now you sit high. If that puts your rack or your cargo into the main wind stream, you could end up with a bunch of noise. They have something under the front bar to help. I would prefer to see how well it works on your configuration. The rack will sit at diffrent heights on diffrent vehicles.
I do like that they offer generic sizes for a good price. If they have the bottom slotted also you could come up with some brackets to bolt it down to your existing holes. That would get you closer to your roof. My rack sits about an inch off mine. Most sit between one and two inch off the roof.