I am in the same boat; when the cutscenes started playing and I knew what was going to happen I thought I'd just ESC out of the cutscenes and then Quit and reload and maybe let the timer run out instead of... doing what I'm supposed to do... but that apparently bogarted things because now I spawn inside the bunker and cannot leave through either entrance (stairs or ladder). As noted, it's impossible to load an "earlier save game" because of the stupid always-saving "feature" of UbiSoft games... so now the game is basically worthless and unplayable unless I start over, which (Jacob being my 3rd target).... ah, no, not "no" but HELLS no.
I hold little hope that this bug will ever be fixed so I guess I am just done with Far Cry 5.... and increasingly "done" with all Ubisoft games and their ****ty save game feature
Hey guys, if you are experiencing this, please create a ticket with your save file to help us investigate.