I think the problem is in the NiStringExtraData property. I'm not sure what it does exactly, but I noticed that the values in this property match the coordinates of the trees in the nif file. I'm pretty sure (but not 100%) that this property is in someway used to render the trees and for relief heights.
I compared nif 2, which places trees on the NE corner of a tile. As you can see in the image, your model (on the left) has much more trees in the bottom left corner, which would appear in the middle of the tile. These are not covered by the NiStringExtraData property. These are also the trees that are missing on your screenshot. (The bottom left of your custom tree batch)
What I did in my models, is keeping the tree arrangement the same as the base file. I deleted some trees of the base file, and move the imported new trees to the location of the deleted trees. As you can see in the screenshot, the bamboo batches are in the same place as some trees of the base file. A benefit of this is that the amount of trees remains the same, so you avoid the forest become too dense of too sparse.
Another benefit of this, is that the shadows are also in the same location. I only had to change the UV coordinates to use the proper part of the dds file. I see that you use the shadows of 2 models at the same time. You see some shadows without a tree.
What do you exactly mean by "Finally it seems that sometimes the worldbuilder doesn't take into account my model"?