"include" means basically you aren't allowed to use files from any other Edain version, but the current.
The dark elves are still part of the game files. Therefore, it wouldn't be a problem for a submod to make them available again.
Using a map which isn't part of Edain anymore and not part of the maps.big would be forbidden, or a model, skin, graphic and so on. That is the main meaning for the rule.
The example of Zaphragor is a bit more difficult. Basically implementing it yourself would be ok, just copying the code might be a problem. (Of course not in this case, but depending on what it is that is readded it might be a more difficult case).
Moreover, as submods have to be allowed first, there might be some special specifications concerning the content. So if we are of the opinion thatZaphragor should never get that ability back, that might be forbidden.