I added an option to the fbx exporter to disable the rotation matrix that is applied to the object transforms during export. With this option disabled only the axis system is written to the fbx file, but the object transforms are left as-is. This leaves it up to the importer on the other side to apply the space transform during import.

Unity has added an import option to apply space transform on import in its latest version, but the current version of setting the axis system in the fbx file and applying the matrix causes unexpected behaviour. Most users will expect that Blender has a forward direction of -Y and and an up direction of +Z (Suzanne is looking in the -Y direction and the "front" view is coming from the -Y direction). But if you set the axis conversion to -Y and +Z the exporter will apply a 180° rotation because it assumes a forward direction of +Y. When done this way, using the new import setting, the mesh will be imported correctly in Unity, but the rotation of the root objects will contain that 180° rotation. Using the +Y and +Z axes during export will import everything without any rotations, but what the user expects to be forward will now be pointing the other direction in Unity.

When we just write the axis system as -Y and +Z to the fbx file and leave the rotations of the root objects untouched we can effectively define any foward axis and have it still be imported correctly, because every conversion will be done on Unitys side. With this patch and Unitys new import option it feels like the first time that using fbx between Unity and Blender works without issues regarding axis conversion.

I also changed the bake_space_transform naming in the UI back to "Bake Transform" to differentiate the two options. But there may be better names for these two options.