with a Pi Zero W with no issues other than occasional hangups of the signalling but that was solved with a software watchdog.
Here are some pics of my setup. I had to de-solder the Waveshare header and solder on a 90 degree header to get this to fit in the frame in a low profile. (Ugh I wish things were sold without headers soldered)
As far as getting hot really fast, the first thing I can think of is if you accidentally plugged in the GPIO rotated 180 degrees -- even briefly -- you might have fried one or both boards.
Second thing I can think of, although it's more likely to just damage the e-Ink rather than make things become hot -- is e-Ink displays don't like to be hot-plugged/unplugged -- you should have all the connections plugged in before switching the system on.
WaveShare, come on, I'm looking at you.