This is intentional, to prevent farming. The strike has always been this way.
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It wasn't 'always' that way I forget exactly when it got changed, somewhere around curse of osiris?, but things did count in the boss room way back before it was changed because it was used as a farming spot.
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The Hollowed Lair strike did not exist during Curse of Osiris. It was used to farm for the Mindbender's Ambition shotgun, but bounties have never progressed in the biss room.
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I don't remember when it changed but they did i used to farm them in there.