Old thread, but kept coming up in my searches regarding Thule cargo boxes that fit, so thought I'd post my findings after a visit to Rack Attack.
Test fit on 2017 4Runner with factory rails and crossbars, crossbars and boxes adjusted as far forward as can go.
Thule Force XL - Rested on antenna and just barely touched tailgate when open. Guys at store said you can grind out the channels and allow the box to adjust slightly more forward to get clearance. It was very close to clearing both.
Thule Motion XT XL - The slope of the back and the channel in the middle allow easy clearance of antenna, about 1-1.5" of clearance to hatch open.
I offset this unit to one side all of the way, clamps loose, the antenna cleared by about a mm or two (no channels outside of the center). When offset, we mocked up a Rocky Mounts Brass Knuckles bike stand next to it and it would mount. Only issue would appear to be the bike pedal on the box side, might have to come off. Didn't try out a bike on it. I am not sure with clamps fully tightened it would fully clear antenna, but again, this could be an option.
The Force felt surprisingly flexible and thin in person. The Motion XT had stiffer plastic, felt sturdier and had a steel piece along the center length of the floor to give additional stiffness. Due to the feel of the units, I went with Motion XT XL. These XL units are bigger than I thought, can hold quite a bit. Also, the XL vs the L in the Motion XT - the XL length seemed to better fit the size of the vehicle aesthetically.
The Yakima Skybox mounting clasps are thicker and not padded, seem like more of an issue mounting on factory bars and scratching your roof. The Skybox felt a lot sturdier, stiffer, thicker, etc than the force. On build alone I would lean Skybox over Force based on what I saw in person.
Hope this helps!