The most heat development is directly in the SoC. If not enough heat can be released to anything acting as a heat sink it feels like a centralized hot spot there.
Yes, without the cover the heat could be released more easily to the environment, but I think there is only a little difference between the first and the actual slim-line case in this concern.
Generally, what I usually see, is when the phone is charged it is mostly laid on its back display facing up. The other way around display down if actually not being used would be better to prevent any heat accumulation.
Worst would be to simply charge it anywhere it actually is (pillow, blanket, pocket etc.). Rather prefer solid surfaces not supporting heat accumulation too much.
There were house and apartments fires due to the cause of overheating phones while being charged and not monitored.
I think it´s rather an internal reason. Not necessarily the cpu/gpu generating too much heat, but the heat release. Some users here did post requests (ideas) for a case fully or partially made of metal. Considering the better heat conduction this may only cause even more burned finger tips. 
I prefer to go with less heat conductive materials, at least for the outer shell.
Generally the design should be optimized to a better thermal balance. On Ifixit I saw that the 2GB storage chip is seated on top of the SoC. This already accumulates more heat as if being separately located.
And there I cannot see much of thermal conductive components which may be supporting for a better heat distribution. I see more potential here to advance.
Hm, 
…aha… it is? Very nice thanks for sharing the link.
I just took a short glance at what the link provides.
Yes, that really sounds great and the required permissions are still acceptable.
An interesting solution someone has found for so many processes which could be done automatically without any user interaction. The principle seems to offer an entertaining playground for those who like to setup their individual automation flows.
the cpu 
