Exhaust and intake are the obvious first things that everybody thinks of, and they should. As said, both are pretty high, so you can already get through quite a bit of water without causing problems there.
However, there's a lot more things to consider.
The engine itself isn't watertight. The engine breather typically is not an issue as it's required by law to be connected to the air intake (for emission control). But you also have to consider the seals on the output shaft, seals on gear shifters, clutch and such. Are your spark plug connections waterproofed or will they short out? Is the o-ring on the oil filler plug still in perfect shape?
Where do your electric cables run? Are all your connections, particularly the ones down low (e.g. kickstand switch), waterproofed? Where does the ECU sit, or the cabling to any accessoires that you may have installed?
Another issue: When your front/rear wheel hub is at ambient temperature and all of a sudden submerged in cold water, the air in the hub will contract and will suck water in from the stream. This will most likely be through the bearings, washing out any lubricant in there. And afterwards the hub will be partially filled with water, with no easy way out.
Then there's the environment to consider. Except in cases of flooding, like in the video, you don't typically find these kinds of streams in urban areas, but in nature reserves. When you cross it, all the road grime, chain lube and other contaminants will wash off and pollute the stream.
And the last thing: The stream you're crossing is typically a river, not a lake. Rivers flow, and when you're more than knee deep in a river, there's not a lot of current required to wash you away.
I'm not saying it's impossible. All I'm saying is that there's a lot more to consider than just the engine air intake/exhaust, when the water is more than, say, axle deep.