The two approaches are not necessarily contradictory. It's more in contrast with the traditional sectoral approach, with each department having its own regulations and no real communication among departments.
That is the main thing with the ecosystem approach. You have to take into account the various policy levels. We go more by that than by the species-by-species approach, although the ecosystem approach does require us to take into account the species-by-species approach.
Basically, the question has to do with where the priorities lie. Clearly, for example, areas where there are species at risk should take priority over an area where there is another ecosystem or another species that is less at risk.