If the project has good separation of concerns, you don't need atomic updates. Good separation of concerns yields many benefits beyond ease of project management. It requires a bit more thought, but if done correctly, it's worth many times the effort.

Good separation of concerns is like earning compound interest on your code.

Just keep the dependencies generic and tailor the higher level logic to the business domain. Then you rarely need to update the dependencies.

I've been doing this on commercial projects (to much success) for decades; before most of the down-voters on here even wrote their first hello world programs.