I quickly checked their website and it's a little unclear (so don't consider this legal advise), but their legal basis is probably the CAO. If that particular CAO has been made mandatory by law (which happens for certain industries that need tighter control from government, like temporary employment agencies), than it automatically applies to companies doing the exact work that's described in the CAO ('werkingssfeer').
It's a shame that RVO and Belastingdienst did not warn you correctly. The Netherlands does not want entrepreneurs, they want everybody cozy at their jobs at some big company.
Do you happen to be in or around Nijmegen with your chip development?