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As the others said, there is no definite answer to this. But here is how we do it:

There is a global schematic library and a global footprint library. They have the components we use and have the necessary details (like references to the ERP system). But there is still only one symbol for different values (i.e. 1 kΩ resistor and 470 Ω resistor use the same symbol). All symbols and footprints are our own footprints. The libraries are text based (KiCad) and are tracked with git. There is a single person that is responsible for the library. Since we don't have too many different parts, we can keep all in the same library. Similar with 3D models. All global 3D models are in a single folder.

Next to that, a project may have its own schematic and footprint library with its own 3D models. In this libraries are parts that are specific to this project, for example a case maybe inside a "footprint", and that case can be specific to a PCB. A other reason to have some parts in a local library is to have a symbol with a different pin layout without everything going into the global library.

> How to deal with footprints of the same type (e.g. QFN64) but with slightly varying dimensions as a result of manufacturer guidelines?

Do they have to be different? Most of the time, the datasheet only has suggestions for a footprint but that doesn't mean you have to follow this.
If you really need different footprints, create a new name, like `SO8` and when you later need to add a different footprint also for a `SO8` component, you may name it `SO8_small`.