There are a lot of linkages between the different depths in the ocean. Even if you're only protecting the benthic system, only the sea floor from fishing, some of the activities that happen in the water column, in the top part of the water, have the potential to affect the integrity of the whole ecosystem. If you're taking out a lot of biomass, some of those might be predators or the bigger fish that eat fish in the benthic area. A lot of these interconnections might be interrupted by allowing fishing in parts of the water column, even if you're protecting the benthos.
That's what the scientific evidence points to. The areas that have no fishing at all, no extractive activities in addition to fishing, have been shown scientifically to be more effective at increasing biomass, protecting biodiversity, and so on.
It doesn't mean that all MPAs have to be fully no-take, it just means that we need to have a portion of our MPA system fully protected.