I would not of wanted to do the swap without the body lift. Its easy and cheap enough to do, why not just do it as per AA recommendation.
As you said, it DEFINITELY helps with clearance-makes things easier all around.
To comment on the second part of that, I disagree. People break D60s, D44s, anything. Its all on knowing how not to be a dumbass in my opinion.
I beat on this TJ pretty hard, AND its on 35s-which the internet wizards said would shatter the Dana 35 instantly. It could last a long time, or 1 day. Kinda like people who talk about motors that are indestructible...there is always someone who manages to blow it up due to being a moron. Now in no way am I saying that the Dana 35 is a great axle, it is far from that. I just don't see a point in changing it until it breaks. (mainly just advice for Ephry73) It reminds me of how the internet world says the AX-5 is the weakest transmission in the world. I have in fact broken one with the weak 2.5L in the TJ...but then again, a good friend of mine who has a OM617 Benz swapped TJ and beats on that to the extreme and has yet to destroy his AX-5 he put behind it, because its simply what he has to use at the time of doing the swap. Crazy.