MASTERMODEL my friend i have the SAME model (esm spitfire 50cc) with the SAME engine (dle 55 ra) with the SAME problem as you have!!!
Problem isnt from inadequate engine cooling. i have my cylinder out like you have and it gets enough fresh air. i have meauserd engine temp and its ok.
Problem seems to come from the combination of rear exhaust with rear carb as you said before and you are right.
Symptoms are exactly the same as in your case. While without cowling engine runs fine but when you put it on, engine seems to rise temp, but its not!
something has to do with the combination of hot air from exhaust coming to the carb. i had another engine before to that plane EME 55 CC version II with side exhaust and engine DIDNT have any problem at all!! what i did was to put some kind of balsa baffling between carb and exhaust like the fellow in post 8 and i also created a vent line from carb to the inside of plane body for a steady pressure reference point. i havent flown plane yet because its very windy here, but motor seems to work fine that way with plane cowling on it. i will inform quite soon, i hope!!