A body lift has no effect on the suspension and will not create any additional issues. It will, however, make it easier to correct or avoid other issues. Keep in mind that advertised lift height and actual lift heigh can vary dramatically depending on the Jeep. OME is highly recommended because they publish their spring rates and offer several spring choices so you can calculate pretty accurately where you will end up. For comparison I currently run the OME springs with a body lift on my LJ with 33s. I have my bump stops set to make full use of my shock travel and have no interference from the fenders. With the body lift I was able to install a raised skid plate and get rid of the ugly stock shovel of a skid while gaining additional clearance. Stock control arms may look flimsy but are well designed and are really very good. I just recently replaced mine and not a single one had any damage. They flex well and are relatively strong. They are also cheap.When you say 3'' of lift as the threshold, are you suggesting that 3'' of suspension lift, or 3'' of total lift?
Would getting 3'' of suspension, and then adding on body lift exceed that threshold and shoot me down that rabbit hole, or would I still be in a safe place?