### 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)

GLuint vertex_array_gl = 0;
				GLuint index_array_gl = 0;
				uint32_t input_mask = 0; 
				if (mesh_instance.is_valid()) {
					mesh_storage->mesh_instance_surface_get_vertex_arrays_and_format(mesh_instance, j, input_mask, vertex_array_gl);
				} else {
					mesh_storage->mesh_surface_get_vertex_arrays_and_format(surface, input_mask, vertex_array_gl);
				}
				index_array_gl = mesh_storage->mesh_surface_get_index_buffer(surface, 0);
				bool use_index_buffer = false;
				glBindVertexArray(vertex_array_gl);
				glBindBuffer(GL_ARRAY_BUFFER, state.canvas_instance_data_buffers[state.current_data_buffer_index].instance_buffers[state.canvas_instance_batches[p_index].instance_buffer_index]);
				uint32_t range_start = state.canvas_instance_batches[p_index].start * sizeof(InstanceData);
				_enable_attributes(range_start, false, instance_count);
				if (index_array_gl != 0) {
					glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, index_array_gl);
					use_index_buffer = true;
				}
				if (use_instancing) {
					if (instance_buffer == 0) {
						break;
					}
					
					glBindBuffer(GL_ARRAY_BUFFER, instance_buffer);
					glEnableVertexAttribArray(1);
					glVertexAttribPointer(1, 4, GL_FLOAT, GL_FALSE, instance_stride * sizeof(float), CAST_INT_TO_UCHAR_PTR(0));
					glVertexAttribDivisor(1, 1);
					glEnableVertexAttribArray(2);
					glVertexAttribPointer(2, 4, GL_FLOAT, GL_FALSE, instance_stride * sizeof(float), CAST_INT_TO_UCHAR_PTR(4 * 4));
					glVertexAttribDivisor(2, 1);