How is the '+ New' menu populated in document libraries?

Digging further into the issue, I compared the source code of the two different configuration options. First with the default setting (but with allow management of content types: yes) and the second one with my custom content type.

As expected, my new content type is rendered as a JSON-object on the page itself, which (naturally) isn't present without the custom content type. But that is the only thing that differs. Everything else on the page source code is equal. 

On an unchanged Document Library, only the default “Document” content type is shown in the source code, but not visible on the “New” button. You see “Word-document” but nut the actual content type “Document” in the library. But wait! What’s happening here? This can’t be right? Can it?

My guess is equal to my previous comment, that the source is different. If you haven’t made any changes to the document types, they don’t show. They are replaced from a different source, since they aren’t present on the page itself. Interestingly when creating a new document library selecting Document Template to “None” or “Microsoft Word Document” (which is default), you get the list of office document template to choose from. Select any other document template, you see the actual content types. Kind of ambiguous, I think.

So the recommendation would be to always add your own content type on new document libraries to avoid possible confusion among our users.