The hero upgrade [far from home] (+15% attack damage when not in room where crystal bot is SLOTTED) deactivates even if the bot is isn't slotted, I tend to keep the crystal bot follow me the entire game and see that the icon briefly appears above my head red and see my damage bonus decreases in the menu.

If it is supposed to deactivate if you're in the same room then it should say ''+15% attack damage when not in the same room as the crystal bot'' 

From Steam: https://steamcommunity.com/app/1485590/discussions/2/3874844033655798408/