As a general idea I'd treat the game + all add-ons as if it was the whole game itself, and make the wiki pages like usual.
The only exception is that I would put a mention about each entry's "restricted" access on of them.
For example, on the data.raw page, I would just add a small icon with a tooltip:
![Image](https://forums.factorio.com/images/ext/2bdd4a9ac45fa758ea351d18a8ff3787.png)
The icon itself might even be a tiny dedicated image so that we could recognize the required add-on without even hovering it.
Here's another suggestion on how the ownership to a specific add-on might be hinted:
![Image](https://forums.factorio.com/images/ext/ad4aba867ea6cae8d99ee47097099604.png)
And finally, here is what I have in mind for looking at all the quality-varying stats in the entity descriptions:
![Image](https://forums.factorio.com/images/ext/0b2a6d27a225138ba70b4d8f6f2a8e36.png)