### Godot version

4.0.1.official

### System information

Windows 10

### Issue description

I wanted to use a multiple atlas textures to crop out a character from a tilemap while saving all animations in one atlas texture and having other atlas textures inherit the first one and crop out the induvidual frames.

But opening the region editor after using the created atlas texture in the new atlas texture shows the original texture scaled to the size of the cropped texture. Using the editor and setting the correct values works just fine and the preview shows the correct result.

Result:
![screenshot](https://user-images.githubusercontent.com/50096015/227557377-da899d85-f7b7-43f1-847c-79f8b27a64ef.png)


### Steps to reproduce

- Open MRP
- Open "character_sprite_1.tres"
- Click on "Edit Region"

### Minimal reproduction project

[AtlasBug.zip](https://github.com/godotengine/godot/files/11063481/AtlasBug.zip)

OS::get_singleton()->benchmark_begin_measure("create_editor_theme");
	Ref<Theme> theme = Ref<Theme>(memnew(Theme));
	
	theme->set_default_base_scale(EDSCALE);
	
	Color accent_color = EDITOR_GET("interface/theme/accent_color");
	Color base_color = EDITOR_GET("interface/theme/base_color");
	float contrast = EDITOR_GET("interface/theme/contrast");
	bool increase_scrollbar_touch_area = EDITOR_GET("interface/touchscreen/increase_scrollbar_touch_area");
	const float gizmo_handle_scale = EDITOR_GET("interface/touchscreen/scale_gizmo_handles");
	bool draw_extra_borders = EDITOR_GET("interface/theme/draw_extra_borders");
	float icon_saturation = EDITOR_GET("interface/theme/icon_saturation");
	float relationship_line_opacity = EDITOR_GET("interface/theme/relationship_line_opacity");
	String preset = EDITOR_GET("interface/theme/preset");
	int border_size = EDITOR_GET("interface/theme/border_size");
	int corner_radius = EDITOR_GET("interface/theme/corner_radius");
	Color preset_accent_color;
	Color preset_base_color;
	float preset_contrast = 0;
	bool preset_draw_extra_borders = false;
	const float default_contrast = 0.3;
	
	
	if (preset == "Custom") {
		accent_color = EDITOR_GET("interface/theme/accent_color");
		base_color = EDITOR_GET("interface/theme/base_color");
		contrast = EDITOR_GET("interface/theme/contrast");
	} else if (preset == "Breeze Dark") {
		preset_accent_color = Color(0.26, 0.76, 1.00);