I don’t know, I guess it’s a matter of the author. My personal recommendation is to use NPM packages, at least for app code and the benefit of portability and modern tools compatibility. But this is not an official core decision. We still maintain Atmosphere packages, and in some cases they are necessary, especially when interacting with the Meteor process lifecycle.
So either way is fine. We can move from one to another in the AI world anytime. I would focus on ensuring compatibility with Meteor 3 in the current format NPM, publish it, and later decide if we want to move. For simplicity, it may be better to split efforts and focus on compatibility first.