Trust me the MT doesn't run hot and I have been using it since it first come out.
All of these recorders give off heat and that heat can build if they are confined. Lithium batteries are temperature sensitive and produce a variable amount of their own heat when discharging..
Lithium batteries age more quickly when exposed to heat. It is a non-issue with the r09's cheap rechargables but a concern with the mt's internal battery.
I got my MT when it first came out onto the market. While the original firmware was buggy, this has long been fixed even though the bad rap continues. I have for a few years made many flawless recordings on it and since I use this recorder almost always for stealth situations, it is simply a matter of having a system in place. For instance, where I keep the unit (usually a phone case on my belt), where the mics are (usually in croakies on my glasses), how I run it (velcroed to the phone case which opens, showing me the screen). After the initial settings, I lock the buttons, which are easy to touch by accident, but easy to touch is a big plus when you do not want to look at the unit or draw attention. I can find all the buttons without looking as the layout is easy too. It is a great recorder. Mine never runs hot, but I usually have an external battery attached (in my pocket, short wire to the unit) , so in fairness it is drawing little or no power from the internal battery. In fact I usually have a full charge showing on the MT at the end of a show. I like the external battery, because I never have to worry about turning the deck on or off while I am at a show and in a stealth environment, that is one more thing to not worry about. Also I have a battery box that plugs right on top the unit (from Sound Professionals), and that way I use the TRS jacks but the mic plugs in through the 1/8 jack.
I have a few other ways I use the deck in less stealthy environments, but again, I have a system and while I keep tweaking things, I don't vary much from show to show and don't ever have any problems.
Most stealth recorder systems work well if the flow is planned out and refined though use.