Under "Room Settings -> Security & Privacy -> Who can ready history?" do you have "Anyone" set? I believe this controls whether it can be indexed or not, as if

Under "Room Settings -> Security & Privacy -> Who can ready history?" do you have "Anyone" set? I believe this controls whether it can be indexed or not, as if you have it on any of the "Members only" settings, their bot needs to be in the room for it to see history. Disclaimer: I'm fairly new to administrating a Matrix server so I could be wrong, but the logic seems to make sense with my suggestion.