I have multiple entry schengen visa from French Embassy in Nigeria. I am presently in Spain; I came into Spain from France. Can I return to Nigeria (country of origin) from any schengen country, specifically from The Netherlands?
Yes. While you are meant to apply for a visa to your main, intended destination country, it doesn't really matter that much once you get your visa. There's nothing to stop you changing your mind about where you go when you get to Schengen. You can travel freely within the Schengen Area and leave from wherever you like. Once you leave Schengen (in your case from the Netherlands) before your allowed stay expires.