You may review the entire documentation for MongoDB regarding Atlas and Self-Managed MongoDB.

The current documentation has some good pages, for example

Self-Managed Configuration File 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(): 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: 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.