The atomicity argument is strong only if your deploy strategy allows it. If you've got anything out there that rolls back on a failure without rolling everything back, or any users that need to pin their version for a while for some compliance reason, or any customers that write code that integrates with your code, or any airgapped deployments that people might update piecemeal, or if you want to open source part of your stack, or if you ever think you might want to do these things in the future, then you're really going to regret creating a culture where nobody is practiced at the care that goes into maintaining backwards compatibility.
Besides, agents really fly when the whole project fits comfortably in their context window. You get all these nice interfaces to bound context with if the API's and public types are defined and versioned separately from each team's repo.