### Godot version

4.0beta13

### System information

Windows10, AMD Ryzen 9 3900XT, RTX3070, Vulkan

### Issue description

I would expect when using the scale tool on an object with a scale of (1,1,1) without touching any of the handles to result in a uniform scale again (i.e. 0.1, 0.1, 0.1) and not one, where all components are different.
However, when the object has been rotated, this is the case no matter if using local or global transform.

![RotateAndScaleBroken](https://user-images.githubusercontent.com/53947784/213452728-d03427dd-be89-4bba-8dba-fbade6627555.gif)

This behavior was working properly in 3.x

### Steps to reproduce

- Create an object (e.g. a CSGBox3D)
- Rotate it a little on different axes
- Scale it with the scale tool, without using any handle (uniform scale)
- Observe how the object is now slightly squashed or stretched, i.e. the scale components are not equal anymore

### Minimal reproduction project

[BrokenScale.zip](https://github.com/godotengine/godot/files/10457086/BrokenScale.zip)

Observe how the cube turns into a pillar when using the Scale Manipulator.
} break;
		case VIEW_HALF_RESOLUTION: {
			int idx = view_menu->get_popup()->get_item_index(VIEW_HALF_RESOLUTION);
			bool current = view_menu->get_popup()->is_item_checked(idx);
			view_menu->get_popup()->set_item_checked(idx, !current);
			_update_shrink();
		} break;
		case VIEW_INFORMATION: {
			int idx = view_menu->get_popup()->get_item_index(VIEW_INFORMATION);
			bool current = view_menu->get_popup()->is_item_checked(idx);
			view_menu->get_popup()->set_item_checked(idx, !current);
		} break;
		case VIEW_FRAME_TIME: {
			int idx = view_menu->get_popup()->get_item_index(VIEW_FRAME_TIME);
			bool current = view_menu->get_popup()->is_item_checked(idx);
			view_menu->get_popup()->set_item_checked(idx, !current);
		} break;
		case VIEW_DISPLAY_NORMAL:
		case VIEW_DISPLAY_WIREFRAME:
		case VIEW_DISPLAY_OVERDRAW:
		case VIEW_DISPLAY_SHADELESS:
		case VIEW_DISPLAY_LIGHTING:
		case VIEW_DISPLAY_NORMAL_BUFFER:
		case VIEW_DISPLAY_DEBUG_SHADOW_ATLAS:
		case VIEW_DISPLAY_DEBUG_DIRECTIONAL_SHADOW_ATLAS:
		case VIEW_DISPLAY_DEBUG_VOXEL_GI_ALBEDO:
		case VIEW_DISPLAY_DEBUG_VOXEL_GI_LIGHTING:
		case VIEW_DISPLAY_DEBUG_VOXEL_GI_EMISSION:
		case VIEW_DISPLAY_DEBUG_SCENE_LUMINANCE:
		case VIEW_DISPLAY_DEBUG_SSAO: