Since this comes up first in googling this, I may also add that at least as of Unity 2020.3.19f1, there is an extra step involved when changing materials, you have to extract the material first. For doing that select the FBX, in the inspector go to Materials and press Extract Materials and then on that extracted material do the unlit cutout setting and etc.
I may be wrong here since you are talking about importing .blend file(s) into Unity but this is what I have to do for importing FBX files into Unity from Blender.
Thanks for the great tool!