Stacked cards are active when cards look for them in that state. Well, maybe active isn't the right word. But there are plenty of cards that say "spot X minions stacked on X card to blah blah blah." So you can spot them in that type of situation. But they can't be spotted by cards that simply state "Spot X minions."
Remember that there are plenty of cards that are exceptions to the rules. After all the rules state that stacked cards are not active. But there are cards that say "If this card is stacked, do X." Obviously that card's text does work while it is stacked because it specifically says so. There was a common saying on Decipher's boards when the game was active: Cards override the rules. If a card states that it can do something and the rules say otherwise, common sense says that the card can indeed do what it says it can do.
Regardless,
No Refuge only works when its owner is a Shadow player. Same with
Troop Tower. Because if their owner is a FP player,
No Refuge and
Troop Tower are inactive and they do not say that they can do anything while in that state.