Just found this thread while searching for something else...
Do you remember how high this rack sits on the topper?
That's my Tacoma in the photo above. I started with a stock Yakima setup:
It was too high, added unnecessary torque to the shell when offroad and, most importantly, wouldn't fit in my garage. I drilled holes through the roof and bolted on a set of Thule load bars:
I attached an identical set of Thule bars to the RTT. When I lower the RTT onto the topper the upper loadbars sit on top of the lower set and are bolted together:
The "lowered" version of the rack handles better on/offroad and fits inside a standard height garage. I sealed the bolt holes with a silicone sealant and haven't had any leaks after many miles of rain and snow. So far, the topper hasn't developed any cracks or other signs of fatigue.