### Godot version

4.1.1-stable

### System information

Windows 10

### Issue description

When the project loads in editor, all the settings defined in project settings will be loaded over the default values, but when running the game nearly 95% of them will be ignored resulting in just loading the default settings.

here it's just loading only 4 variables from project setting and i have added the fifth in this pull request https://github.com/godotengine/godot/pull/80151
![image](https://github.com/godotengine/godot/assets/53877170/926168a6-e6d3-4983-b59d-7fd202db681d)

Vector<uint8_t> index_buffer;
		index_buffer.resize(p_indices.size() * sizeof(int32_t));
		{
			uint8_t *w = index_buffer.ptrw();
			memcpy(w, p_indices.ptr(), sizeof(int32_t) * p_indices.size());
		}
		glGenBuffers(1, &pb.index_buffer);
		glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, pb.index_buffer);
		GLES3::Utilities::get_singleton()->buffer_allocate_data(GL_ELEMENT_ARRAY_BUFFER, pb.index_buffer, p_indices.size() * 4, index_buffer.ptr(), GL_STATIC_DRAW, "Polygon 2D index buffer");
		pb.count = p_indices.size();
	}
	glBindVertexArray(0);
	glBindBuffer(GL_ARRAY_BUFFER, 0);
	glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, 0);
	PolygonID id = polygon_buffers.last_id++;
	polygon_buffers.polygons[id] = pb;
	return id;
}
void RasterizerCanvasGLES3::free_polygon(PolygonID p_polygon) {
	PolygonBuffers *pb_ptr = polygon_buffers.polygons.getptr(p_polygon);
	ERR_FAIL_COND(!pb_ptr);
	PolygonBuffers &pb = *pb_ptr;
	if (pb.index_buffer != 0) {
		GLES3::Utilities::get_singleton()->buffer_free_data(pb.index_buffer);
	}
	glDeleteVertexArrays(1, &pb.vertex_array);
	GLES3::Utilities::get_singleton()->buffer_free_data(pb.vertex_buffer);
	polygon_buffers.polygons.erase(p_polygon);
}
void RasterizerCanvasGLES3::_allocate_instance_data_buffer() {