For a flute it'll make minimal difference if it's plastic or clay or bone. You can find endless discussions on this on flute- and whistle forums, but it all boils down to the fact that the sound is produced by a standing wave of air inside a tube, and not by any vibrations of the actual tube material (i.e. totally different from string instruments). Though the material can make a difference when it comes to the actual part where you blow across an edge (very minimal differences are audible - and working with different and more or less difficult materials affect this). (I own flutes and whistles made of plastic or other synthetic materials, various types of metal, and wood)
fantastic stuff. I'm fiddling with screenshots from your  link video to try to pull 3D model from multi-image 3d model build tools. I too would very much like a print of their playable reconstruction on my desk. Please update if you get to a usable STL.