### 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(PropertyInfo(Variant::INT, "display/window/size/window_width_override", PROPERTY_HINT_RANGE, "0,7680,1,or_greater"), 0); /
	GLOBAL_DEF(PropertyInfo(Variant::INT, "display/window/size/window_height_override", PROPERTY_HINT_RANGE, "0,4320,1,or_greater"), 0); /
	GLOBAL_DEF("display/window/energy_saving/keep_screen_on", true);
	GLOBAL_DEF("display/window/energy_saving/keep_screen_on.editor", false);
	GLOBAL_DEF_BASIC(PropertyInfo(Variant::STRING, "audio/buses/default_bus_layout", PROPERTY_HINT_FILE, "*.tres"), "res://default_bus_layout.tres");
	GLOBAL_DEF_RST("audio/general/text_to_speech", false);
	GLOBAL_DEF_RST(PropertyInfo(Variant::FLOAT, "audio/general/2d_panning_strength", PROPERTY_HINT_RANGE, "0,2,0.01"), 0.5f);
	GLOBAL_DEF_RST(PropertyInfo(Variant::FLOAT, "audio/general/3d_panning_strength", PROPERTY_HINT_RANGE, "0,2,0.01"), 0.5f);
	PackedStringArray extensions;
	extensions.push_back("gd");
	if (Engine::get_singleton()->has_singleton("GodotSharp")) {
		extensions.push_back("cs");
	}
	extensions.push_back("gdshader");
	GLOBAL_DEF(PropertyInfo(Variant::PACKED_STRING_ARRAY, "editor/script/search_in_file_extensions"), extensions);
	_add_builtin_input_map();
	/
	custom_prop_info["display/window/handheld/orientation"] = PropertyInfo(Variant::INT, "display/window/handheld/orientation", PROPERTY_HINT_ENUM, "Landscape,Portrait,Reverse Landscape,Reverse Portrait,Sensor Landscape,Sensor Portrait,Sensor");
	GLOBAL_DEF("display/window/subwindows/embed_subwindows", true);
	/
	custom_prop_info["display/window/vsync/vsync_mode"] = PropertyInfo(Variant::INT, "display/window/vsync/vsync_mode", PROPERTY_HINT_ENUM, "Disabled,Enabled,Adaptive,Mailbox");
	custom_prop_info["rendering/driver/threads/thread_model"] = PropertyInfo(Variant::INT, "rendering/driver/threads/thread_model", PROPERTY_HINT_ENUM, "Single-Unsafe,Single-Safe,Multi-Threaded");
	GLOBAL_DEF("physics/2d/run_on_separate_thread", false);
	GLOBAL_DEF("physics/3d/run_on_separate_thread", false);
	GLOBAL_DEF_BASIC(PropertyInfo(Variant::STRING, "display/window/stretch/mode", PROPERTY_HINT_ENUM, "disabled,canvas_items,viewport"), "disabled");
	GLOBAL_DEF_BASIC(PropertyInfo(Variant::STRING, "display/window/stretch/aspect", PROPERTY_HINT_ENUM, "ignore,keep,keep_width,keep_height,expand"), "keep");
	GLOBAL_DEF_BASIC(PropertyInfo(Variant::FLOAT, "display/window/stretch/scale", PROPERTY_HINT_RANGE, "0.5,8.0,0.01"), 1.0);
	GLOBAL_DEF(PropertyInfo(Variant::INT, "debug/settings/profiler/max_functions", PROPERTY_HINT_RANGE, "128,65535,1"), 16384);
	GLOBAL_DEF(PropertyInfo(Variant::BOOL, "compression/formats/zstd/long_distance_matching"), Compression::zstd_long_distance_matching);
	GLOBAL_DEF(PropertyInfo(Variant::INT, "compression/formats/zstd/compression_level", PROPERTY_HINT_RANGE, "1,22,1"), Compression::zstd_level);