With or with out lids you will need ventilation and top ventilation is very inefficient. There are pros to no lids and pros to with lids with is faster to clean to be sure. And a much bigger pain for everything else.
I small recess for the flexwatt is not a bad idea I think you will find a sander better as it is less than 1/16 thick. I would router a place for the t-stat probe however.
I would also suggest that you keep the room at 80 cooler is hard to keep the temps correct the ambient air temp is almost a;ways the room temp give or take a degree or two. There are a lot of people whom have had issues with keeping warm side temps in rooms around 75º not even talking about cool side temps.
Ideally flexwatt is not run over 100ºF for very long, that limits the room temps a lot.
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