For example, maybe krill do a poor job recovering nutrients from dead krill, while they do great job of it with whale waste. In this case, whales would keep the overall amount of nutrients available to krill high while also consuming them.
Who knows what's actually going on here, but it's really not difficult for these sorts of highly interrelated systems to end up with counterintuitive dynamics.
Phytoplankton convert sunlight and dissolved CO2 into biomass, krill eat phytoplankton, baleen whales eat krill. So the role of the whale poop is fertilisation. https://en.wikipedia.org/wiki/Iron_fertilization
For instance: Krill need chemical X when young but create it when older in large quantities. Wales poop out X then. Or wales create X, while krill do not.
Another possibility is recycling. Suppose the rate of iron addition via dust seeding is A tons per day, the rate of iron lost when a krill dies of old age is 60% and the rate of iron lost when a krill is eaten by a whale is only 30%. If the average age of krill dropped by say 20% then the biomass of krill should significantly increase.