Significant Update - water leak appears to be fixed. We've gone through a rain event and no leak. One of the spots where sealant was applied was the wiring for the awning entering the coach.
Bigger update. We found the source of the smoke and it wasn't the HVAC units despite smelling it at each. On our last outing, we ended up having an issue of smoke when not just the front unit running but the rear as well. We shut both down and ran on the roof fans planning on just driving home despite being there not even a day. Sometime later that evening we realized that we were running on battery power. Despite cycling the shore breaker and even changing to 30 amp, no power was coming in.
Fast forward a couple of weeks. Accessed the EMS, tested, and even talked with Progressive Industries with an end conclusion that the EMS was operating correctly. The next focus was the ATS. Sure enough the negative lead was the problem. The wire got hot enough that it melted the whole shore terminal block, insulation on both hot leads, and melted an aluminum bus / terminal bar on the shore. The HVAC units were just circulating the smoke and were never the source. I'm thinking a loose connection on the negative lead.
We have a replacement ATS on its way. Fair warning for those with the 50 amp Intellitec ATS, they are not currently producing them as they are being redesigned. Most places are out of stock.
Moral of the story - make a plan to check your wiring terminations that use mechanical connections. I'm planning on checking the EMS, ATS, main distribution panel, inverter/converter and genset connections annually.