We aren't here to give you legal advice. We are not lawyers. Again, if it's legal there and in your destination... You're probably going to be fine and you're worrying about nothing. If you're that worried check the webpage for the Netherlands security agency and see what is forbidden on planes. You could hit some message boards that are actually in Dutch and see if they can answer your question more thoroughly. Did you buy it in a shop there or have it mailed to you? You really probably have nothing to worry about. It doesn't sound like you're planning on taking pounds of it with you. Just enough for a day or two... That isn't a lot. Put it gel capsules and put it in a container and label it "Kratom Tea Powder". Then you aren't misrepresenting what it is. Really, it sounds like you are worrying about nothing.
I'm suggesting that you take it before you clear security and then have some in your carry on as an herbal supplement or tea (because that's what it is). I don't foresee any issues boarding the plane unless security is really intense in NL... Which to my memory, it isn't. Do you live in the NL? Are you familiar with how airport security works there?