Microsoft has published a whitepaper with an official guidance on modifying pre-defined content types.
You can find the white paper here:
The whitepaper includes possible alternatives for modifying the content types and also a list of known issues that can occur if pre-defined content types are modified.
The most important part is the conclusion:
We recommend that you do not change pre-defined content types in SharePoint Products and Technologies unless there is no other alternative. We recommend that you create new content types that are based on pre-defined content types, and change the new content types instead.
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