Has nothing to do with the expansion and contraction of metal, it's the air and gear oil. Here's how it plays out in a stock setup - the diff rotates, gear oil gets hot and expands, air gets hot and expands, extra air is pushed out the jiggle valve on the top of the diff, all good. Go to cross water above the axle, the cold water cools the gear oil and air enough to cause a contraction, the vacuum slams the jiggle valve shut and no water gets in, there's not enough vaccum to compromise the axle seals, all good. Fast forward a couple years, gear oil sloshes around and creeps up inside the jiggle valve, attracts dust, jiggle valve gets clogged and stops jiggling, not so good. Now when the oil and air heat up and need to expand, the jiggle valve doesn't relieve the pressure. The axle seals are normally the next weakest point, and air and gear oil will push through them - out, not in. But enough of being compromised like that will weaken them, and if you hit the next river with weak axle seals and a clogged jiggle valve you do stand a good chance of sucking water through the axle seals (or the jiggle valve, if it's clogged open), and that's got the potential to be very bad indeed depending on how much water gets in.
Answer number one is keep the jiggle valve clean and stay out of water above the centerline of the axle - your owners manual has a fording depth for your 4Runner for a reason. If you have to cross water much higher than that infrequently, a functional jiggle valve should still keep you in good shape, but it's a good idea to check your gear oil after. If you are crossing higher water frequently, or super deep water at all, extending the breather (and keeping it clean) is cheap insurance against water intrusion, but you should still check your gear oil frequently.
So explain how the cold water completely skips cooling the diff and goes instantly to cooling the fluid? The giant cast iron housing is going to act like a giant insulator to the fluid. Y'all are talking about super cooling the fluid instantly. Ain't gonna happen.