A904 real seal questions

To Measure; all 4 wheels need to be on the ground and the suspension at normal ride height.
If the rear wheels are hanging,
the rear end has swung forward on the front spring segments and pushed the driveshaft forward.
In the pic, I agree that the rubber boot should not be touching the yoke, which would burn it off in no time.

I can't say for sure but IMO the boot is not there to keep dirt out of the seal. IMO it's there to collect any ATF leaking past the seal, and drip it out the little hole at the bottom, onto the street, instead of all over the bottom of your car.
That it keeps the dirt off the seal is IMO just a bonus.

In years gone by, it might have made it possible to drive thru water deeper than the tail, but that was like 80 years ago. If you drive thru water that deep, yur gonna have lotsa other worse problems.

I could be wrong and I don't care. If mine doesn't have a hole, I drill one.