See the part of the flower stem I marked with red color, that part is behind the flower transparent petals mesh, I was thinking that part would not be rendered unless I set the alpha discard threshold. Probably I am missing something!?
The order that the triangles render is all the difference… whether it’s because of JME sorting two objects back to front or because the mesh itself presorts them back to front.
For example, one common way to deal with double-sided transparent boxes is to double the faces and have the inside faces at the beginning of the buffer and the outside faces at the end. So the inside faces are always rendered first.
If your flower only has one material then it’s one mesh and it must be that the stem triangles are drawn first. If the stem also has transparent parts then you should be able to get them to obscure the petals by looking at the flower from different (low) angles.
If your flower has more than one material then it is two geometries and JME is just sorting them correctly.