The scale setting in the Spine texture packer settings only reduces the texture resolution, not the skeleton size.
We don't maintain the GameMaker Studio runtime ourselves so I'm not sure how it works. I've never used it either.
But normally, there is a setting in your chosen editor that allows you to set the skeleton import scale.
For example, the Spine-Unity runtime uses a 1% scale by default because 1 Unity physics unit is 100 pixels/Unity sprite units. But this number is editable.
You probably just need to look for the setting in GMS.