### Godot version

4.0 beta 15

### System information

Windows 10

### Issue description

When ticking `apply_root_scale` the scale is not applied to custom collision shape set in importer.
This apply for `shape_type`  Box, Sphere, Cylinder and Capsule

_I tried to fix it myself but i'm a bit confused on how to have acces to the `apply_root_scale` and `root_scale` at the moment where the shape is generated_

### Steps to reproduce

- Add a 3d model.
- Generate physics for the mesh
- Select a `shape_type` for example Box
- Add `root_scale` != 1 and tick `apply_root_scale`

### Minimal reproduction project

[BoxColliderImport.zip](https://github.com/godotengine/godot/files/10500751/BoxColliderImport.zip)

Transform3D transform;
	ShapeType generate_shape_type = SHAPE_TYPE_DECOMPOSE_CONVEX;
	if (p_options.has(SNAME("physics/shape_type"))) {
		generate_shape_type = (ShapeType)p_options[SNAME("physics/shape_type")].operator int();
	}
	if (generate_shape_type == SHAPE_TYPE_BOX ||
			generate_shape_type == SHAPE_TYPE_SPHERE ||
			generate_shape_type == SHAPE_TYPE_CYLINDER ||
			generate_shape_type == SHAPE_TYPE_CAPSULE) {
		if (p_options.has(SNAME("primitive/position"))) {
			transform.origin = p_options[SNAME("primitive/position")];
		}
		if (p_options.has(SNAME("primitive/rotation"))) {
			transform.basis = Basis::from_euler(p_options[SNAME("primitive/rotation")].operator Vector3() * (Math_PI / 180.0));
		}
	}
	return transform;
}
#endif