Choosing the "Custom Identifier" option under Setup Step 1.1 in conjunction with "Custom identifiers will be used to identify published items" in Setup Step 4.3 works poorly when the journal publishes continuously, ie. creates and publishes a container issue, and subsequently publishes articles within that issue. 

If the journal is using the "Public ID" (custom identifier) field in the issue's Table of Contents to create the article's DOI, that ID is only used as the DOI when:

-- the issue is published;
-- the "Reassign DOIs" button in Journal Setup Step 1 is pressed. 

If the issue is already published, and the article is scheduled against that issue and given a Public ID, the ID won't be used as the DOI without reassigning all DOIs -- something Editors won't necessarily know how to do, or have access to do, as it is in the JM domain. 

Possible solutions:

1) add "use as DOI" button next to public ID field in Table of Contents which, when pressed, will (re)assign the current Public ID as the DOI (clunky, UI-wise); 
2) maybe add something to the scheduling section in the submission's Editing interface, although I can't possibly see how this would be less clunky than 1); 
3) automatically assign the DOI if the Save button on the ToC page was pressed, and the value for the Public ID previously was null.