There is no limitation for the scale compensate setting in the Maya FBX Plug-in itself.
However, there is a limitation in 3ds Max. If you modify the scale of joints that are parents of other joints in Maya, they do not import correctly into 3ds Max. This import problem occurs because 3ds Max does not support Maya’s scale compensate attribute.
If you scale a parent joint in Maya using scale compensation, it creates an offset for child joint rather than scaling it.
But if you do the same thing in 3ds Max, the child scales and creates no offsets.
Since 3ds Max does not support Scale Compensate, any joint hierarchy you use in Maya with scale compensate looks wrong in 3ds Max.
Deactivate scale compensate for joints only if you have modified the scale of any joints that are parents of other joints.
If all your joints are the same scale, you do not have to deactivate this setting in Maya.
To deactivate scale compensate in Maya:
This deactivates the scale compensation setting.