Wheel size, rotor size
I think that the SR5 and the Limited have identical brake systems. The Sport Edition has slightly larger front rotors, which makes it more of a probelm for aftermarket wheels to fit over them.
The biggest issue I have seen as I am also shopping for winter wheels, is that there is a large positive offset on the 4th gen 4runner stock wheels (+30mm on my Limited wheels). This is a bit over an inch of offset. If you are moving to an aftermarket wheel 16", with zero offset (a lot of the aftermarket wheels seem to be zero offset) this will probably create rubbing problems when turning the wheels fully to the lock. A lift will help, but still if you increase the tire diameter, the rubbing will likely come back.
So I have been waiting for an OEM set of wheels for under $350 to pop up on eBay, someday. I'll just fit the same size tires, but with a winter tire like Blizzaks, they are available 265/65R17.