For reference, an older (pre-67) VW bus will hold a LOT on its roof... At least 4 hippies with an appropriate rack. There's a particularly iconic photo from Woodstock with a bus sporting two hippies and NO rack on a section of roof that I can tell you from intimate experience has little to no reinforcement (just an air box for inner structure). Buses are nowhere near as reinforced as 4runners and have much thinner steel. It's all about spreading the load.
If you're carrying everything across two cross bars mounted to two donut hole-sized points, yeah you're pretty limited. Spread it out across four otherwise identical cross bars and you're able to carry considerably more. Think about the forces that must be tolerated to handle a full rollover. There's a section immediately behind the sunroof that has very little reinforcement, but excepting that there's quite a bit of structure above the headliner.
From the racks I've seen, the Whitson rack looks like it's likely to be able to bear the heaviest load (depending on how it's mounted), and the fact that it's made so specifically for the 4Runner gives it even greater potential from what I can gather.
EDIT: I went to Whitson's profile and found threads he's started, and I see what he's doing. There's potential, I feel, for a much greater load bearing capacity but the design is pretty good. I'd still like to know if there's been any load testing to see what it can actually hold without hurting anything, but I don't think (given that the support at the front isn't going to be bearing much load due to the open area immediately behind it) it should be able to hold much more than the stock rack can without significant modification... I have an idea for a pretty serious expedition rig, and the Whitson rack looked pretty perfect at the surface... Still could be, but would require a lot of modification to serve as the base...