So I did stop by the dealership and tech says "intake and exhaust aren't going to bother me usually... now if you come in with a problem that might be due to exhaust and I can't get to it because something is welded on, then we have a problem
. Also, if I see a tuner, we have a problem".
Another thing I realized is - on the subject of CAI and Tuners - with my last truck it got to a point where I could switch back to factory intake in like 20 min (Mostly because I went through a handful of different brands looking for perfection). So when it comes to these you can do a quick switch for bringing the truck in.
Of course my last truck was a good F-150
and here was a little less hardware for CAI.