You're exactly right that the generals have been clear that they aren't going to interfere in the election or let themselves be used in a coup, which makes the turnover at the Pentagon even more mystifying. A military coup is out of the question, and an attempt at a soft coup using the mechanisms of the Electoral College seems doomed to fail.
Militias, however, are something to keep an eye on. The founder of Oath Keepers said yesterday that they wouldn't recognize a Biden presidency as legitimate. It's hard to know what form that will take, but the Patriot Movement's history of violence is a concern. So far the election has gone off with less violence than I feared, so we may get to the inauguration without a wave of violence, but I do think we're likely to see at least a few standoffs between feds and militias during Biden's term.