### 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)

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_DECOMPOSE_CONVEX) {
		Mesh::ConvexDecompositionSettings decomposition_settings;
		bool advanced = false;
		if (p_options.has(SNAME("decomposition/advanced"))) {
			advanced = p_options[SNAME("decomposition/advanced")];
		}
		if (advanced) {
			if (p_options.has(SNAME("decomposition/max_concavity"))) {
				decomposition_settings.max_concavity = p_options[SNAME("decomposition/max_concavity")];
			}
			if (p_options.has(SNAME("decomposition/symmetry_planes_clipping_bias"))) {
				decomposition_settings.symmetry_planes_clipping_bias = p_options[SNAME("decomposition/symmetry_planes_clipping_bias")];
			}
			if (p_options.has(SNAME("decomposition/revolution_axes_clipping_bias"))) {
				decomposition_settings.revolution_axes_clipping_bias = p_options[SNAME("decomposition/revolution_axes_clipping_bias")];
			}
			if (p_options.has(SNAME("decomposition/min_volume_per_convex_hull"))) {
				decomposition_settings.min_volume_per_convex_hull = p_options[SNAME("decomposition/min_volume_per_convex_hull")];
			}
			if (p_options.has(SNAME("decomposition/resolution"))) {
				decomposition_settings.resolution = p_options[SNAME("decomposition/resolution")];
			}
			if (p_options.has(SNAME("decomposition/max_num_vertices_per_convex_hull"))) {
				decomposition_settings.max_num_vertices_per_convex_hull = p_options[SNAME("decomposition/max_num_vertices_per_convex_hull")];
			}
			if (p_options.has(SNAME("decomposition/plane_downsampling"))) {