2013 Thor Tuscany 45LT
2nd owner of this rig and I have the same issues. I have scoured the internet for the same advice, but I can't find anything online.
I have begun the process of caulking everything in the rear bathroom, and it has helped a great deal, except that the caulk is sticky enough that it collects the soot that still comes into the space. We have made it a routine for cleaning mode to kick in when we arrive at our destination. At this point, I am down to the areas that didn't get enough caulk or areas that now allow the soot to enter, because the old areas are sealed. After I get the interior done, I will work with Great Stuff to get the underside sealed. The worst intrusion I had was at the top of the shower wall. I had a technician look at the issue, and he claimed it was mildew. Upon closer inspection, I could see the shoddy caulking job somebody attempted in order fix the problem.
Oh, don't worry about not getting the work done under warranty, because if my rig is any indication, they just used Great Stuff in the front cap, and it looks like a third grade art project that received an "A" for "Almost!"