When a building gives me trouble when collecting, I (ab)use the swipe collect. I mean I start with a different building, for example residence, and continue the swipe over the area with small problematic building. (I play in the app, but I assume “swiping” works similarly in the browser.)
As for the whole set collect - if it’s hard coded, I’m also against it. My reason is the same - event quests. It’s not just about CCs. It’s about collecting goods as well. For example I can leave my Jester’s Tavern intentionally not collected (gives T3 goods), while keeping collecting Reveler’s Fountain (gives mana or seeds). It’s one set.