I'd like to think the first part is talking about making extensions to the code, that you should be writing subclasses to add new functionality for your own use

I'd like to think the first part is talking about making extensions to the code, that you should be writing subclasses to add new functionality for your own use, not maintaining a series of patches. That is, dependency injection for your extensions, not alterations to the core. The whole project reeks of anachronistic development practices, though.