Theory: The 25th has already been invoked by notice delivered to Pelosi/Grassley. They’re not making it public because they don’t want to risk inflaming the situation in DC. And they are still working out who presides over Electoral Vote count if Pence is Acting Prez.
Maybe it's like Cheney giving orders from his bunker on 9/11. Military is just assuming that Pence has Trump's backing when he speaks, because he always has in the past.