### Godot version

v4.0.2.stable.official [7a0977ce2]

### System information

Windows 10

### Issue description

The settings found in **application/config/project_settings_override** end up being written to the `res://project.godot` every time the editor is started.

I find this inconvenient, `res://project.godot` is always on the changelist in git because of this.

I think it would be better if settings with the same value as found in **application/config/project_settings_override** were persisted in `res://project.godot` **only** when set by the "editor interface" or "by code" and not by the "merge" that happens at the start of the editor.

### Steps to reproduce

1. Before opening the MRP in the editor, note **window/size/mode** value within `res://project.godot`;
2. Now open it in the editor and check the `res://project.godot`, notice that **window/size/mode** was changed by the contents of `res://project_override.cfg` (which is the **application/config/project_settings_override** file).

### Minimal reproduction project

[Projects Override Merging Into Project Godot.zip](https://github.com/godotengine/godot/files/11555239/Projects.Override.Merging.Into.Project.Godot.zip)
GLOBAL_DEF_BASIC(PropertyInfo(Variant::DICTIONARY, "application/config/name_localized", PROPERTY_HINT_LOCALIZABLE_STRING), Dictionary());
	GLOBAL_DEF_BASIC(PropertyInfo(Variant::STRING, "application/config/description", PROPERTY_HINT_MULTILINE_TEXT), "");
	GLOBAL_DEF_INTERNAL(PropertyInfo(Variant::STRING, "application/config/tags"), PackedStringArray());
	GLOBAL_DEF_BASIC(PropertyInfo(Variant::STRING, "application/run/main_scene", PROPERTY_HINT_FILE, "*.tscn,*.scn,*.res"), "");
	GLOBAL_DEF("application/run/disable_stdout", false);
	GLOBAL_DEF("application/run/disable_stderr", false);
	GLOBAL_DEF_RST("application/config/use_hidden_project_data_directory", true);
	GLOBAL_DEF("application/config/use_custom_user_dir", false);
	GLOBAL_DEF("application/config/custom_user_dir_name", "");
	GLOBAL_DEF("application/config/project_settings_override", "");
	GLOBAL_DEF("application/run/main_loop_type", "SceneTree");
	GLOBAL_DEF("application/config/auto_accept_quit", true);
	GLOBAL_DEF("application/config/quit_on_go_back", true);
	
	
	
	
	GLOBAL_DEF_BASIC(PropertyInfo(Variant::INT, "display/window/size/viewport_width", PROPERTY_HINT_RANGE, "0,7680,1,or_greater"), 1152); /
	GLOBAL_DEF_BASIC(PropertyInfo(Variant::INT, "display/window/size/viewport_height", PROPERTY_HINT_RANGE, "0,4320,1,or_greater"), 648); /
	GLOBAL_DEF_BASIC(PropertyInfo(Variant::INT, "display/window/size/mode", PROPERTY_HINT_ENUM, "Windowed,Minimized,Maximized,Fullscreen,Exclusive Fullscreen"), 0);
	/
	GLOBAL_DEF_BASIC(PropertyInfo(Variant::INT, "display/window/size/initial_position_type", PROPERTY_HINT_ENUM, "Absolute,Center of Primary Screen,Center of Other Screen,Center of Screen With Mouse Pointer,Center of Screen With Keyboard Focus"), 1);
	GLOBAL_DEF_BASIC(PropertyInfo(Variant::VECTOR2I, "display/window/size/initial_position"), Vector2i());
	GLOBAL_DEF_BASIC(PropertyInfo(Variant::INT, "display/window/size/initial_screen", PROPERTY_HINT_RANGE, "0,64,1,or_greater"), 0);
	GLOBAL_DEF_BASIC("display/window/size/resizable", true);
	GLOBAL_DEF_BASIC("display/window/size/borderless", false);
	GLOBAL_DEF("display/window/size/always_on_top", false);
	GLOBAL_DEF("display/window/size/transparent", false);
	GLOBAL_DEF("display/window/size/extend_to_title", false);
	GLOBAL_DEF("display/window/size/no_focus", false);