Sorry for the delay in replying, I've been very busy at work the last days.

Here are the steps you need to take:

Firstly, modify your all tree ref models, also the same that are copied 1:1, that did not repeat as references, eg. more or less vertexes and tris.

This needs to be done, because the WED FBX Importer make it automatically as referenced ("as model ref") and after converting you got the same rotation, this is wrong, right?

1. Select All Objects (Ctrl+A)
2. Menu -> Group -> Group -> OK
3. Hierarchy panel -> Adjust Pivot rollout -> Affect Pivot Only
4. F12 and set the XYZ axis to 0, close and deselect the Affect Pivot Only
5. Right Click on (Select and Rotate) and in Absolute:World set the X to -90
6. Menu -> Group -> Ungroup -> OK and Select All Objects (Ctrl+A)
7. Utilities panel -> Reset XForm -> Reset Selected
8. Export it as Up Axis: Z-up, Done!

Now the 270° is gone, but should be possible with the FBX Importer also, just ask Developers.