In the Content Type Hub I have the following two content types:
Company Document:

and Collaboration Document which is inherited from the Company Document. Notice the difference in required fields:

Due to strict security policy here at the company, I had to hide parts of the names.

I have a custom Document ID provider developed, deployed and configured.

Scenario:

• A new site collection gets created. A couple of custom libraries with Collaboration Document content type are added to the site by a feature receiver.
• Both content types (Company Document and Collaboration Document)
  look fine (configured exactly the same as in the Content Type Hub)
  in Site Content Types and in Library Content Types.
• For the Document ID to work with the Content Types from the Hub, I need to go to Content type publishing, select Refresh all published content types on next update and click Ok. Otherwise Document ID Generator event receivers won't be added to the content types. After running Content Type Subscriber job everything is fine and the Document ID starts working.

The problem is that the content type Collaboration Document gets updated in all the libraries and it looks like this:

(sorry for the change in branding). So it inherits required fields from its parent content type Company Document and not from the content type that it is supposed to inherit from (Collaboration Document). To add more confusion, the site content type looks like this:

(which is absolutely fine). So its fine at the site level, but it
messes up at list level. If I create a new list AFTER refreshing the
content types from the hub, the libraries seems fine and the required
fields are configured how they are supposed to be.

Inherits is set to True as this is a requirement.

Does anyone have any thoughts on this? How can I make sure that the
required fields are based on the correct content type? Or maybe is there
a way how to get Document ID working without doing the Refresh all published content types on next update?

Any help appreciated.