I've been tinkering with the same concerns for a year or two (meaning that I've dumped thousands of dollars into proposed solutions). Bottom line, is that adding anything to the top of your Jeep (rack & or RTT) is going to dramatically change the fuel economy and ride dynamics involved. It will also be noisy, no matter what. At first you will think that these changes suck. You must embrace the suck!
Have you removed the top from your JK for a trip? Try it and you will notice that it feels much more "sporty" and agile. On a two door that top weighs less than 100 lbs. Put that top back on, add a 75 lb rack, then a 150 lb RTT....the "sporty" is gone and then some.
The best money spent will be upgraded suspension and anti-sway hardware. When I had an RTT and Slimline II rack on the worn-out stock suspension, driving my Jeep was scary. It simply ruined road trips. My Jeep used to be all about the journey. With a rack & RTT, you need to be looking forward to the destination, because the journey is going to involve keeping both hands on the wheel when you hit frost heaves. White-knuckled terror.
Not really, my JK is tolerable now. I went with an AEV suspension, but I suspect that an OME overland kit would be a better choice. If adding a 75 lb rack was enough to suck some joy out of driving your JK...any RTT (plus the rack weight) is likely to kill that joy entirely. I really don't think that lowering your rooftop gear by 1.5 or 2 inches will make any difference.
Ultimately, having an RTT on a JK means that you will be driving no more than 65 MPH in any conditions that are less then ideal. Frost heaves will scare you. You will need to keep two hands on the wheel at all times and you will probably be getting appr. 16 MPG on average. Others may report different experiences, but adding a rack and/or RTT will change your JK. There is no "magic solution".