Since this involves another mod, I'll post the same thing there.
( https://mods.factorio.com/mod/atan-air-scrubbing )
When I put the level three pollution module into a beacon, the Air Scrubbers' max pollution filtering (-100 at legendary) gets reduced by 80% (-20%).
tldr, it probably doesnt take the negative polution into account and subtracts the % of the pollution module?