### 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)

}
						}
					}
					if (mesh_settings.has("generate/shadow_meshes")) {
						int shadow_meshes = mesh_settings["generate/shadow_meshes"];
						if (shadow_meshes == MESH_OVERRIDE_ENABLE) {
							create_shadow_meshes = true;
						} else if (shadow_meshes == MESH_OVERRIDE_DISABLE) {
							create_shadow_meshes = false;
						}
					}
					if (mesh_settings.has("generate/lightmap_uv")) {
						int lightmap_uv = mesh_settings["generate/lightmap_uv"];
						if (lightmap_uv == MESH_OVERRIDE_ENABLE) {
							bake_lightmaps = true;
						} else if (lightmap_uv == MESH_OVERRIDE_DISABLE) {
							bake_lightmaps = false;
						}
					}
					if (mesh_settings.has("generate/lods")) {
						int lods = mesh_settings["generate/lods"];
						if (lods == MESH_OVERRIDE_ENABLE) {
							generate_lods = true;
						} else if (lods == MESH_OVERRIDE_DISABLE) {
							generate_lods = false;
						}
					}
					if (mesh_settings.has("lods/normal_split_angle")) {
						split_angle = mesh_settings["lods/normal_split_angle"];
					}