I don't think it's made clear in the article (but my Dutch is very limited and I may have missed something)... but my assumption was that the separation of arriving and departing passenger is something that will only happen in the non-Schengen zone. If my assumption is right then I don't think it's a bad thing as it will eliminate all those additional security checks that shouldn't really be necessary but that are currently required because Schiphol mixes departing and arriving passengers.

Someone who has cleared Security at another EU or Schengen airport should NOT have to clear security again at Schiphol... but mixing with arriving non-EU passengers makes these passengers "unclean", hence the need for re-screening. Having central security, and sending arriving non-EU/Schengen transfer passengers through security on arrival, should make things a lot more efficient.