No sense fretting or holding your breath, folks. I just posted what the book says and what's recommended especially since it made me change what I do. Sometimes I take recommendation and information and don't follow it 100%. I probably freak out over questionable safety information more than others. That's my choice and I don't want to turn blue in the face to follow it.
Being under enough vehicles and trailers, I've noticed that more times than not, there can be the tiniest of a slight gap between the round of the U-bolt and the axle. This is why I think jacking from the U-bolt jammed it up against the axle even more and this caused the nuts to loosen and who knows what I did to the axle (no problems so far and it's been 4-5 years). I don't jack from the u-bolt and at the last few torque checks, things were snug as they should be ever since.
If you want to jack up from the u-bolt, the frame, the brake drum or the axle, then so be it. A forum is a great place to post all information found for each person to develop their own sense that works for them from as much information as possible. Others have built metal "cups" to use at the U-bolts, some lift from the frame. Just learn enough to be comfortable and safe and it's not always the easy way.
Btw - my Keystone dealer also told me Missions were fine and I could tow overweight (by about 1,200 lbs). I chose otherwise as I learned more (ended up buying a newer truck but still was 300 lbs overweight), but I currently own Marathons as I continue to learn and legally changed out the rear end to completely solve being overweight. Now I've learned even more and have equipment that means I will jack up at the frame and no longer think about it. I will continue to pass this on if someone asks. I am not THE answer man in this forum, I am only one member of this forum trying to provide the best answer for a question.
This is a perfect example of what Jack Nicholson meant when he said, "You can't handle the truth". A manufacturer covers their rump because some individual caused them some major hardship and cost and they just don't want to afford a repeat. If they change their documentation to state this and I'm not smart enough to know why, and I'm able to get the equipment to follow their recommendation, then it's what I've done. Many times the changes are subtle because the public can't handle the truth and the panic is horrible. I won't go into examples of this, but I will mention Ford Explorer and Firestone tires - Has anyone rented from U-Haul lately, locations where I live will not rent trailers to Ford Explorer owners, even today, wow, really> It's panic!
I posted this because purely stating to go ahead and jack at the u-bolts is probably not the only thing to post. One should post what's the safest (manufacturer's documentation), then what else has been done and why. I've read too many wheel, tire, and suspension mishaps that tells me this concern isn't worth it for me. So I can't comment on whether this is an issue or not, so I just follow the recommendation since the OP asked what to use and it's helpful if we also add how and why.
Obviously, typing all this, I've been breathing fine. I wish you all the same. Collectively, we have answered the OP's question thoroughly.