Every time the rear suspension moves up or down, the driveshaft moves in and out of the trans. If that boot did not have a hole, imagine what it would be doing. The hole is there to prevent that. The boot is just there to keep the yoke relatively free of debris to help the seal live..
Since the seal is "breathing", whatever it inhales, in needs to exhale it as well, else it may damage the proper seal. I have always pointed it down or nearly so.
That makes me your Fourth witness. and now you have an idea why, instead of just my opinion.