First item, brakes shouldn't be making noise. Either turn up the heat on them or take it to a new dealer. Item two, you need to do a better job of isolating/pinpointing where the noise is coming from as there are literally hundreds of possible places that could have an issue. Plus, it's virtually impossible to help if we, or they have no clues. If you go to a dealer and tell them there is a squeak/rattle but offer no area/location for them to focus on, they will go for a drive and see if it occurs. If it makes noise and they can pinpoint it, they will probably fix it, but if it doesn't and this will most likely be the case as of now, you will pick it up, the repair invoice will say "couldn't replicate problem". Do your best to give the guys something to work with, it'll help both you and them.
*I have noticed that on severe bumps/potholes, that the rear brake cables will slap against the leaf spring. You *could* be hearing this, but them again you've got discs and I haven't seen the cable routing, so maybe not. Maybe have a look and see if this is possible. Look for marks on the cable.