The bug you have when looking at the back of your trees is what we call a "alpha sorting problem".
It happens with non binary alphas.
I don't know where it lies in the nadeo importer workflow, here are some things to try:
Save manually your transparent texture as DXT1, not DXT5, this will force the alpha channel to be binary (=Black OR white, no grey).
But the DXT1; to gain memory space, uses a trick : it removes alpha channel and "paste" it in the diffuse : the transparent pixels are black. (this causes a black halo on border pixels).
If this fixes your problems, you will have to create sources with binary alpha (you'll need to contrast the alpha channel until it's only Black and White).
If DXT1 doesn't fix it, the bug is elsewhere.
Our images are saved as non binary alpha, but we specify somewhere in our datas that they will displayed as binary, the engine convert the 256 grey alpha to black and white ( dark greys are read as black, light greys as white).
So, our own .dds will probably create the alpha sorting bug if used in a material not forcing the binary Alpha, as you tested.
That also means that a texture with non binary alpha in a mod will be read as binary, because or material will force it.
This has annoyed a lot of mod makers when we converted stadium, because they were no longer able to create glass/ice effects by just applying a grey alpha, but this choice is also more robust and avoids your kind of problem.
My conclusion : I think the items transparency shading doesn't force binary alpha (this enable players to do more complex things like smoke, but I'm not sure it's "wanted"), so any "NotReady" texture will create this sorting bug.
Note : in the past(10 years ago O_O) Binary alpha was not forced in the engine but directly read from the image, and sometimes it was really hard to get photoshop reach the binary state.
We could contrast, contrast and contrast again the alpha channel...photoshop always let 1 pixel or 2 being different than black or white... that gave me headaches.
Trick 1 :if you don't find a way to have your sources as you want, save as DXT1, reopen it and copy the alpha channel into your source. (It's quite simple, maybe a script or plugin exists, or a more simple way to do it with more recent tools)
Trick 2: in photoshop, uses the free filter
freebies : solidify A to expand the color of your diffuse in the transparent areas, to avoid outside pixels drooling (although it doesn't work well with foliage, it's better to clone your tree in transparent areas to maintain crispyness in the mipmaps).