While I can see that there are downsides to central security (such as the one you mentioned), the main problem with the setup at Schiphol is that huge amounts of time and resources are currently being wasted on additional security checks for people who don't need them.

Anyone who has cleared security on the same day, at an airport in the EU and/or the Schengen area, should NOT have to go through security again. At the moment transfer passengers, except on Schengen to Schengen transfers, are having to waste time on additional security checks that would not be needed if Schiphol didn't mix arriving and departing passengers. All this time-wasting could be avoided if the departure area were turned back into a secure area, with transfer passengers from outside the EU/Schengen being sent through security checks on arrival.