You may review the entire documentation for MongoDB regarding Atlas and Self-Managed MongoDB.
The [current documentation](https://www.mongodb.com/docs/) has some good pages, for example
[Self-Managed Configuration File Options](https://www.mongodb.com/docs/manual/reference/configuration-options/): It clearly states, this page is valid only for Self-Managed MongoDB and does not apply for Atlas.
Other pages are not so clear and especially for beginners they can be very confusing.
For example [db.createUser()](https://www.mongodb.com/docs/manual/reference/method/db.createUser/): Command `db.createUser()` does not exist on Atlas, however this is not mentioned at all in this page.
Another poor example is [Deploy a Self-Managed Replica Set](https://www.mongodb.com/docs/manual/tutorial/deploy-replica-set/): Despite the headline refers to Self-Managed MongoDB, in the middle and all of a sudden the page provides an instruction to create a replica-set on Atlas. This create more confusion rather than clarity.