The core idea is that most endings from the new content work independently and won't mess with your original choices, which is pretty convenient if you're trying to experience everything. You can wrap up the spy story stuff and still go for whatever ending you were planning in the main storyline

There's this interesting twist though - if you make specific choices with songbird and reed, you'll unlock what they call the tower path. It happens when you either hand songbird over to reed during killing moon or if you side with reed first and then spare songbird later in somewhat damaged. Going down this road changes things pretty dramatically, and once you start those follow-up missions like who wants to live forever, you're basically committed to that path

Something worth keeping in mind is that the tower really shakes things up - v ends up in a coma for two years, loses their cyberware stuff, and it completely changes how your story can end. You can't go back to the original endings once you're on this track but you'll get some unique rewards like reed's special gun. For all the other endings though, you're free to finish things however you want just make sure you really want the tower before going for it since it's a pretty big commitment that changes everything