In that comment I was referring to a study that showed the five criteria that have been shown to create the most effective MPAs. The last one was that they should protect whole ecosystems or be, as the study says, isolated by deep water or sand. In other words, it means if you protect a whole rocky reef or a whole ecosystem, that's going to be more effective than only protecting a tiny proportion of it.
If you're thinking about a whole ecosystem, then making sure you don't just slice the ecosystem into small pieces and protect a tiny portion of it is what leads to more effective biodiversity conservation.