People have been jacking on the diff housing for ages, and they have been doing it "wrong", "lazy", "easy", "simple" for ages that way too. It is a "lawyers" sentence, but not only because of the safety in jacking. (It is considered sufficiently safe to jack any vehicle with two tires down, but three tires is obviously safer.) The second reason the attorneys say not to jack using the differential is because they really do break sometimes because of it. And Ford does not want to pay for new differentials under warranty, or trying to fix malfunctioning ones from pumpkin shell deformation because rear end lifting that way.
If you really look at it, its a lot of weight on the front to back edge of the shell, right at the cover location. And the cover itself is NOT a rigid structure providing support to the pumkin shell for several reasons. First the cover is not very strong, its stamped steel or aluminum that is not structurally strong. Second its just bolted on, and not tightly. e.g. There is a gasket there (paper or silicone) that is DESIGNED to give (in order to be maleable to do its actual job, stopping leaks out of the cover / pumbin join. Its is not a structure support element. This means the pumbkin can flex, and gets very little support out of the cover.
95% of the time, if it flexes, it flexes back (at least enough) so that you don't have any ill effects. But 0.001-5% of the time, the flexing does not entirely recover, and it adds up. So lift that way over a long period of time, over 10-20 years, you might end up with a problem. Ford does not want to pay for even one unit in the warranted 3 years, or sometimes 7 for powertrain, so they void the warranty if the diff fails, and they can prove you lifted it that way. Dealers don't (usually) lift them that way, they have lifts. But plenty of even certified mechanics do it that way because its convenient. If it fails, they will just lie and its the customer's problem.
The wording is designed to head off the small number of failures (but perhaps 1%) from home mechanics not smart enough to lie, and who then say, "it doesn't say "don't do that" in the manual. Well, it does say don't do that in the manual, so that Ford will win that battle.....
If you break it, its an expensive repair or replace. So, I just jack on the axle about 2/3 of the way out to the tire. 1/3 to the tire, 2/3 to the differential. And then the other side. The closer the jack stands are to the tires, the more stable the lift, but the most stress on the tube. The closer to the diff, the least stress on the tubes, but the least stability in the vehicle on stands. Also the closer to the tires, the less incline there is during the second lift, and thus the least sideways vehicle movement as you tilt the vehicle up on the jack the second time (and are resting on one stand, tilted above the stand.) I like about 2/3 out (e.g. 1/3 point nearest the tires.)
These days, I just use a T-bar ($55 bucks Harbor Freight) and lift the back via the two axle tubes simultaneously, near the diff, on either side. Then I slide in jack stands at the 2/3 out mark (1/3 near the tires) on each axle, and lower as carefully and gently as I can onto the stands.
Though 98% of the time, you can lift just fine using the diff pumpkin shell, do you really want to be that 2% of the failures? Its all on you then, as Ford definitely will not pay for it, and that is the REAL reason for the language in the owner's manual. TO cover the 2% of the time when the shell bends too much, or cracks. With that language, its NOT on Ford, its on you. Their (Ford's) problem is solved, and yours have just begun.