Fallout London does have a dedicated installer on GOG separate from the main game (and they provide instructions on how to downgrade the game so it remains compatible with fallout london and to run it as a separate game instance), so you do have options even if you play before/after this update drops.

I basically had two installs for fallout 4 - base game + mods, and the Fallout London full conversion + mods. I could switch between them on the fly.