EDIT: also see https://news.ycombinator.com/item?id=23076929
Basically just never go more than 24 hours without backing up, one is none, keep multiple offsite backups, etc.
I don't think Apple was in any way naive about how hot Intel chips can run under load. It's also not impossible to make a laptop body that can run those chips with decent temperatures... if you're willing to make compromises on size.
IMO, the biggest issue was they still chose to make the systems thin in spite of the thermal tradeoffs that would result from that.
Yes, thinner's probably more desirable, but would people have stopped buying MBPs if they were a little less thin? I don't think their sales would have shrunk by much, since most Mac users are for the most part a captive audience, because they love MacOS.
It seems like for the 2016 MBP, they either made significant last minute changes or moved up the release date by several months. When they released the computers the Apple stores didn't even have the right screwdrivers to open them for several months. That doesn't seem like something that was planned, but rather the result of some sort of timeline shift.
My guess is that they decided they needed them out the door before Christmas and so skipped the last six months of QA. Maybe it was something else, but I think it was more than just being unwilling to compromise on size.
Regardless, the 2020 models are basically flawless so far, so at least there's that.