The problem isn't the heat of the battery itself charging (although that adds to the problem), it's the laptop itself generating heat that it can't get rid of which then heat soaks into the battery (amongst other things). The hard drive, processor, memory chips and so on all add to the heat load.
The base of the laptop acts as a heatsink and of course there are ventilation holes and fans, and the duvet blocks those holes.
In case you don't notice the heat, the fans working flat out should be a clue.
If I use my MacBook Pro on a table both fans run at around 2,000rpm and nothing gets above 60degreesC (the processor and the ram chips get the closest).
If I use it on the duvet (or to a lesser extent my lap) the fans will cycle up to their full 5,000rpm+ and stuff begins to hit over 80degreesC.
I've killed 3 batteries in the MacBook by (I believe) doing that. I also believe the problems reported by others are caused by the same actions.
My previous battery lasted a lot longer than the first two, but I was careful when I got that one to only use it on a table. As the4 months went by I got complacent and started using it on my lap and on the duvet. Over the coming weeks the battery health indicator started to drop and drop and battery life dropped with it, eventually going from 4.5 hours on a full charge to just 2 hours. This wasn't helped by the fans spinning faster than normal (even when I started using it on a table again) due to the heat from the failing battery.
Lithium Ion batteries are charged using very carefully controlled current and voltage, get it wrong they heat up and explode. As such you can't over charge one, and it doesn't matter if you let it run down or not. However, you should not let it run completely dead as a doornail flat, that will damage it. There is a reserve built into the MacBook batteries to stop you from doing that (and probably others too). You can start recharging at any point (as there is no memory effect unlike older NiMH type batteries) but it is considered good practice to charge them up fully and let them run down all the way (until the machine sleeps automatically) every once in a while.
