I thing the weight is OK. However, the width and length might be a stretch. The factory roof rails are a bit over 40" wide. The length is similar.
The ratchet ties will need to wrap around and under and without and something to stop it shifting side to side, it might just get a bit cocked eyed on you.
My other concern would be the over hang front to rear. It's a similar issue with no way to really secure. At freeway speed it can have a fair amount of lift and it might just take a flight on you.
It's only about 5' wide and 7ft long, so you might be able to add might find something at a vendor like Yakima to add to the OEM rack.
If it's a infrequent trip, U-haul Trailers are cheap. Around hear a 5'x8' trailer is less than $20/day. You will probably save that on gas if it's a long haul. Dropping a 100 lb paddle boat on a freeway will cost you a lot more and could hurt someone.
In theory it will hold it. The bottom of the hulls will probably sit on the rack itself and not even touch the crossbars (which are the weak point in an already weak system). Long ratchet straps over the boat and under the main rack will probably work, but maybe add some sort of cushion between them. As itr1275 mentioned, the front must be tied down to the front of the 4Runner. I worked in the windsurfing industry for years, and the number of boards and racks that peeled off the top of cars because they weren't tied down to the front of the cars was frightening You are liable if your load comes undone no matter what causes the failure.
It's going to hang over the edges some but weight wise you are good to go. I can't remember the exact dynamic weight limit on factory rails/cross bars but its higher than the weight of the boat (but not by much from what i remember). just make sure the boat is positioned where its balanced and you don't have to worry about it tipping forward and punching a hole in your sun roof... all that aside as long as you strap it down well you will be good to go.
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2011 SR5 | Billstien 5100s (2.65" in front, 1.5" spacer in rear) | 265x70x17 BFG KO2s | RCI metal works full skid system | Victory4x4 sliders and rear window storage | Rhinorack pioneer platform and backbone rails on the roof