I think there's two separate things going on:
As others have noted, S3 sleep isn't supported, only S1 "sleep to idle" sleep. But I don't think this is the direct cause of the overheating. In S1 sleep, the laptop can average something like 900mW of power usage, which is enough to annoyingly knock a few percent off your battery overnight, but not enough to make the laptop warm, even in a bag.
The seems to be a second problem, specific to Windows, that when in S1 sleep sometimes the power consumption is high (of order 10W), and this causes the laptop to get very hot if not well ventilated. I've never been able to figure out if this Windows actually doing something useful in "modern standby" like Windows Update, or whether it's a bug. Edit: And I should add, it's crazy that there's not a way to disable this if it is doing something "useful".
Either way, under Linux the latter doesn't happen, and the laptop sleeps very cool ... just with the annoying "lose 5% of your battery overnight" problem from sleeping in S1.