You are correct that the index entry does not include the _id field by default. Indexes that expressly include _id as a key (which includes, of course, the always-present _id index) do have the _id field. Perhaps you are thinking of the recordID, which is an internal field in indexes used to find the actual document(s).
So, my question is: How do indexes find the main document in MongoDB if they are not using the main index
_id?
Indexes, including the always-present _id index, use the internal recordID to find the document(s) that the index entry points to.