Advocate II
You can pull off the limited trim. Some guys simply remove it completely, and spray bomb the panel behind it black. The couple of pictures i've seen of that looked a bit janky though. The other option is installing the trail or offroad trim piece in its place.Yes, it definitely does. I thought about trimming it if I can find a good place to do so. Otherwise, it will stay until it can't anymore.
Look through http://www.toyota-4runner.org/5th-gen-t4rs/ . You're not the first to deal with fitting armor on a Limited edition, it can be done, just a few extra steps, and some extra limitations.
My understanding is that most limited editions come with 18 or 20" tires, which is another thing I'd definitely be looking at changing. You're much better off with a 17" tire if you're doing any type of serious offroading.