To try to avoid the need for scene merging, we adopted an approach where levels were divided into rooms and then each room was comprised of 10 or so sub scenes which would be baked together at build time. This meant a designer could work on the enemy placement in a room while an artist worked on the light in the same room and they could both check in without any conflicts.
It also meant build a bunch of tools to support such a system. Here You can see our map editor, which we used to manage the flow of the rooms throughout a level. It had automatic preview image generation and was the main tool level designers used to select what they wanted to work on and to note their progress. Artists and designers never had to manually create or open scenes.