### Godot version

v4.0.3.stable.mono.official [5222a99f5]

### System information

macOS Monterey 12.6.6 (21G646)

### Issue description

When creating a tileset by code with custom data layers, removing a layer with `remove_custom_data_layer` does not update the name-to-layer mapping; `get_custom_data_layer_by_name` will continue to return that layer's original index.

This has a downstream effect of causing TileData objects attempting to use `get_custom_data('Layer B')` to return invalid data (whatever custom data is now in Layer B's old index; e.g. Layer C).

I would expect that after using `remove_custom_data_layer`, I would be able to still use `get_custom_data_layer_by_name` on that tileset.

### Steps to reproduce

Run this code to see that getting Layer B by name after removing the first layer continues to return its original index (1) when in reality it is now at index 0.
```
	var tileset:TileSet = TileSet.new()

	tileset.add_custom_data_layer()
	tileset.set_custom_data_layer_name(0, 'Layer A')
	tileset.set_custom_data_layer_type(0, TYPE_INT)

	tileset.add_custom_data_layer()
	tileset.set_custom_data_layer_name(1, 'Layer B')
	tileset.set_custom_data_layer_type(1, TYPE_STRING)

	print('Layer index 0 name : ', tileset.get_custom_data_layer_name(0)) # Layer A
	print('Layer index 1 name : ', tileset.get_custom_data_layer_name(1)) # Layer B
	print('Layer B is on index : ', tileset.get_custom_data_layer_by_name("Layer B")) # 1

	print('----- removing custom data layer 0 -----')
	tileset.remove_custom_data_layer(0)

	print('Layer index 0 name : ', tileset.get_custom_data_layer_name(0)) # Layer B
	print('Layer index 1 name : ', tileset.get_custom_data_layer_name(1)) # prints an error, as expected
	print('Layer B is on index : ', tileset.get_custom_data_layer_by_name("Layer B")) # returns 1 still! should return 0.
```

### Minimal reproduction project

[RemoveCustomDataLayer.zip](https://github.com/godotengine/godot/files/11804762/RemoveCustomDataLayer.zip)

return use_texture_padding;
}
Vector2i TileSetAtlasSource::get_atlas_grid_size() const {
	Ref<Texture2D> txt = get_texture();
	if (!txt.is_valid()) {
		return Vector2i();
	}
	ERR_FAIL_COND_V(texture_region_size.x <= 0 || texture_region_size.y <= 0, Vector2i());
	Size2i valid_area = txt->get_size() - margins;
	
	Size2i grid_size;
	if (valid_area.x >= texture_region_size.x && valid_area.y >= texture_region_size.y) {
		valid_area -= texture_region_size;
		grid_size = Size2i(1, 1) + valid_area / (texture_region_size + separation);
	}
	return grid_size;
}
bool TileSetAtlasSource::_set(const StringName &p_name, const Variant &p_value) {
	Vector<String> components = String(p_name).split("/", true, 2);
	
	Vector<String> coords_split = components[0].split(":");
	Vector2i coords = TileSetSource::INVALID_ATLAS_COORDS;
	if (coords_split.size() == 2 && coords_split[0].is_valid_int() && coords_split[1].is_valid_int()) {
		coords = Vector2i(coords_split[0].to_int(), coords_split[1].to_int());
	}
	
	if (coords != TileSetSource::INVALID_ATLAS_COORDS) {
		
		if (!has_tile(coords)) {