Quick reminder : Atomic Design is a methodology, invented by Brad Frost and based on the idea that designing interface should always rely on the smallest part of the interface (atoms) in order to build any other assets.
The most important aspect is to understand the team, its culture and way of working, its maturity and talk about it, openly and frankly. This is just one way of many ways of doing it. How are you doing it?
The reality is that the design industry is extremely dynamic and the context can switch quickly and it's the same for the design team. Nothing will be perfect — everything can be perfected.