I think I’m wrong with suggestion of ‘open air’ type of walls, as I realize now that your mesh is for ‘internal CFD’. Internal CFD means that your walls are not ‘leaking’, as normally a pipe or a tunnel will not leak water or air. So your setup is not common.
If you were using ‘external CFD’, using Zero Gradient walls for top and left / right sides of your tunnel (which will be BMB [Background Mesh Box]) with similar function to your external box now, would make sens.
I do not know if missing thermal results in simulation with 4 custom walls was due to that custom wall setup.
From previous convergence plots I see that you can shorten the simulation time by 50% without much impact on results. So you are back to mistery of heat accumulation on the top of your box, which in any case looks lake having too big gradients.