I would like clarification about two items in the rules that can be interpreted in more than one way:
1) Magic cards spaces. It is unclear whether by placing a magic card on the left or right side of the board the effect can only be used with the corresponding side limbo or freely with either limbo. For example, if the magic recruitment card (+5) is near the dark limbo edge, can it still be used to recruit from the light limbo (one limbo only, but not the one adjacent to the card)? The rules for the card are ambiguous, and the picture examples are not conclusive.
Does not matter. It is just for convenience how they are laid out. There isn't a distinction between your light and dark sides once the game gets going.
2) Region Cards. It appears that as long as you have an army on one side of a region and the corresponding region card you can use it to attack the other side of the region (because of army in your side of the region enables region card play) with an army adjacent to it on the fighting side, and still get the inhabitants as allies (even though it's the other side). Is that your interpretation?
Not completely following the question. What do you mean by "other side" - like Light vs Dark? Yes, if you occupy the light side Region for example and have the Region card, and have armies adjacent to the corresponding Region on the dark side, then you can use that as the attacker so that the Inhabitants are on your side. Just remember that you need to be adjacent or open up a portal so you can be adjacent.
3) Bonus question -- I assume that when scoring VP each region and province on light and dark are treated separately, as if they were separate "regions" and "provinces."
Correct, they are considered separate region for scoring. If you have 2 of an Area in the Light and the other 3 in the Dark, it does NOT count for having all 5 regions in that area for 3VP.