### 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)

decomposition_settings.plane_downsampling = p_options[SNAME("decomposition/plane_downsampling")];
			}
			if (p_options.has(SNAME("decomposition/convexhull_downsampling"))) {
				decomposition_settings.convexhull_downsampling = p_options[SNAME("decomposition/convexhull_downsampling")];
			}
			if (p_options.has(SNAME("decomposition/normalize_mesh"))) {
				decomposition_settings.normalize_mesh = p_options[SNAME("decomposition/normalize_mesh")];
			}
			if (p_options.has(SNAME("decomposition/mode"))) {
				decomposition_settings.mode = (Mesh::ConvexDecompositionSettings::Mode)p_options[SNAME("decomposition/mode")].operator int();
			}
			if (p_options.has(SNAME("decomposition/convexhull_approximation"))) {
				decomposition_settings.convexhull_approximation = p_options[SNAME("decomposition/convexhull_approximation")];
			}
			if (p_options.has(SNAME("decomposition/max_convex_hulls"))) {
				decomposition_settings.max_convex_hulls = p_options[SNAME("decomposition/max_convex_hulls")];
			}
			if (p_options.has(SNAME("decomposition/project_hull_vertices"))) {
				decomposition_settings.project_hull_vertices = p_options[SNAME("decomposition/project_hull_vertices")];
			}
		} else {
			int precision_level = 5;
			if (p_options.has(SNAME("decomposition/precision"))) {
				precision_level = p_options[SNAME("decomposition/precision")];
			}
			const real_t precision = real_t(precision_level - 1) / 9.0;
			decomposition_settings.max_concavity = Math::lerp(real_t(1.0), real_t(0.001), precision);
			decomposition_settings.min_volume_per_convex_hull = Math::lerp(real_t(0.01), real_t(0.0001), precision);
			decomposition_settings.resolution = Math::lerp(10'000, 100'000, precision);
			decomposition_settings.max_num_vertices_per_convex_hull = Math::lerp(32, 64, precision);