To match with the usual Unity export parameters from blender try the following:
- In the transform/Apply Scaling, select FBX Unit Scale (to fix the scaling issue from the fbx)
- Select the apply Transforms (just in case, to apply any modification being done)
If you also made changes to the armature (like bone creation or removal), maybe redo the armature within the rig menu of the fbx in Unity.
See if all of that helps.