What you're doing is correct.
That scale only refers to the ratio between pixels (Spine editor units) and Unity world units.
1
means 1 pixel per 1 Unity world unit.
0.01
means 100 pixels per 1 Unity world unit.
Currently, having a skeleton data scale around 0.01 is ideal for Unity.
This is mostly for it to fit with Unity's built-in physics whose internal default and maximum values are built supporting that scale. This is also the default scale for native 2D Unity sprites (expressed as 100).
Otherwise, it could be anything you want.