### 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)
ERR_FAIL_COND_MSG(!props.has(p_name), "Request for nonexistent project setting: " + p_name + ".");
	
	props[p_name].initial = p_value.duplicate();
}
void ProjectSettings::set_restart_if_changed(const String &p_name, bool p_restart) {
	ERR_FAIL_COND_MSG(!props.has(p_name), "Request for nonexistent project setting: " + p_name + ".");
	props[p_name].restart_if_changed = p_restart;
}
void ProjectSettings::set_as_basic(const String &p_name, bool p_basic) {
	ERR_FAIL_COND_MSG(!props.has(p_name), "Request for nonexistent project setting: " + p_name + ".");
	props[p_name].basic = p_basic;
}
void ProjectSettings::set_as_internal(const String &p_name, bool p_internal) {
	ERR_FAIL_COND_MSG(!props.has(p_name), "Request for nonexistent project setting: " + p_name + ".");
	props[p_name].internal = p_internal;
}
void ProjectSettings::set_ignore_value_in_docs(const String &p_name, bool p_ignore) {