You never mentioned the fact that HKL was inop. If you brought it to them before for this same concern, then this explains the miscommunication. If this is the case the tech should have checked a very common issue and probably would have solved this the first go round. Should probably ask your service consultant if they checked the sun roof drains in the rear. Lots of techs water test the vehicle and the condition is not right for the leak to occur(could be a particular angle the truck sits on). Therefore they cannot explain the leak so they blame a trunk seal. I have also seen body vents let water in while driving.

As for the key thing. I have personally handled many many BMW owners(all CAS cars) that do not fully understand how to shut the key off, leave it in the vehicle(comfort access cars), function the remote with out knowing ect...
So yes givin all the known info and not knowing that a outside influenced compromised the system, and not a system defect, that is why I went the route I did.
Owners insight on problems in there vehicle, is a great asset in diagnosis and never said that it is not.