You could apply this rule more generically and remove any monster (and really any other type of card, for that matter) that doesn't make sense (use your judgement) in a given scenario, then build the location decks from the remaining cards.
And if you wanted to include a certain card (Aldern Foxglove, for example), you could count the number of cards of each type required for that scenario, add the cards you want to be included, add the rest as random cards from the box, then populate the locations with its required number. In essence, handle each card type with a specific card in it like you do Villains, but instead of 1 per location, you would use the number listed on that location card.
I think this would significantly increase setup time, but it may interest those people who want a more thematic feel.
That is one of the nice things about this game. If you want to spend a little extra time on it, you will be rewarded. I suppose you could also sort through some of the other cards, like barriers for example, and remove some to maintain the theme. Or even do the same with some allies.