Importing FBX files in Unity with the correct scale, rotation, and axis is fraught.

FBX files seems to be in cm by default, but can support other units. Other unit scales are achieved in FBX by by setting GlobalSettings→Properties70→UnitScaleFactor property in the file. For example, a 1 meter cube in 'meters' should be stored in an fbx file like:

GlobalSettings:
  - Properties70:
      - UnitScaleFactor = (100.0)   # The 'unit' is 100 * 1cm 
CubeObject:
    - Lcl Scaling = (1,1,1)

This file will show up in Unity's importer as '1m (File)'.

In order to achieve the above scaling (scale of 1 on objects, UnitScaleFactor=100), in the export settings set one of the following for Transform→Apply Scaling:

• FBX Units Scale
• FBX All

In the FBX file format, global axis alignment is stored in the global properties:

Name: P - String("UpAxis")  String("int")  String("Integer")  String("")  I32(2)  
Name: P - String("UpAxisSign")  String("int")  String("Integer")  String("")  I32(1)  
Name: P - String("FrontAxis")  String("int")  String("Integer")  String("")  I32(1)  
Name: P - String("FrontAxisSign")  String("int")  String("Integer")  String("")  I32(1)  
Name: P - String("CoordAxis")  String("int")  String("Integer")  String("")  I32(0)  
Name: P - String("CoordAxisSign")  String("int")  String("Integer")  String("")  I32(-1)  
Name: P - String("OriginalUpAxis")  String("int")  String("Integer")  String("")  I32(-1)  
Name: P - String("OriginalUpAxisSign")  String("int")  String("Integer")  String("")  I32(1)