Backpacker
Sorry chum, but you've just displayed a shocking lack of knowledge of the flight safety culture prevalent in military aviation. You would be only too aware of this if you were actually involved yourself, rather than making aspersions based on no first hand knowledge. My experiences of both sides have shown the flight safety systems and ethos in the miltary to be far more effective than those present in private flying. I think you'll also find that private flyers are responsible for far more zone/level busts than the military, and the systems in place to ensure military aviators are aware of all relevant NOTAMs are far more rigourous than for private flyers.
I can't speak for Dutch procedures, but relating the incident to UK ops, I can well understand what might have happened - although I am obviously very much guessing here. The F16s may well have reported "not above 1000ft", and, upon hearing of your colleague, descended lower in order to aid visual acquisition of him, by skylining him - it's far easier to see aircarft above the horizon than those below it. I can't recall ever getting a clearance to fly at 1000ft in the UK, but have many times been instructed to fly "NOT ABOVE 1000ft". Liek I say, that explanation is pure supposition on my part, but an educated guess.