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It's not ideal, but it's the lesser of two evils. If someone comes up with another algorithm that prevents players from using flying units to bypass and visit objects past the shifted guards, the developers will consider it. But for now, this is how it is.
And in this case, the system is not perfect in certain circumstances. For example, here I was able to capture an object and Pandora without defeating its guards https://clips.twitch.tv/RoundHyperWerewolfPipeHype