A body lift is just like any other mod. If you do it wrong it might cause trouble. The negative image of body lifts is from tweakers who try and make their own.
A body lift is a lot more than just spacers. It's bumper brackets to relocate the bumpers, it's a steering extension to lengthen the steering column, and fan shroud brackets to relocate that. It takes a full day to do one right, because you have to disconnect tons of stuff to make sure it does not get damaged when you lift the body.
I've never had an issue with one because I've done them right. I've had them on three Toyota's, now that I'm looking at a Raptor, I see no reason not to do one. I've talked to a guy on the East Coast who has done them on two Raptors without issue, and he's driven them hard. He put pictures on another site of him jumping his.
The reason I want a Raptor is the suspension. I've driven two and ridden in several. The best performance (for what I want to do) is stock settings, but that's based on what I like. So the only way to run a 37 tire without changing the suspension or rubbing the fenders is a body lift.
I know there are a lot of negative opinions about body lifts. I don't know how many are based on personal experience, and how many are based on something they saw or heard about, but don't know for sure what was installed or how it was installed. As I said, I'm coming from the Toyota world where you see everything from wood block body lifts, to Performance Accessory and 4Crawler body lifts installed properly.
Here's a view into Toyota world of a Tacoma with a body lift getting flogged hard:
I would not recommend asking the dealership to do it if they don't regularly do body lifts. In fact, I would not be anybody's guinea pig. As Linexsa said, it's a lot of detail work. Find out who in your area does them on a regular basis and talk to them about it. You can also do it yourself. There is nothing hard about it, just time consuming because of all the little detail stuff. Set aside a weekend. But a pro should be able to do it in less than a day.