### 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)

state.canvas_instance_batches.clear();
		return;
	}
	
	glBindBuffer(GL_ARRAY_BUFFER, state.canvas_instance_data_buffers[state.current_data_buffer_index].instance_buffers[state.current_instance_buffer_index]);
#ifdef WEB_ENABLED
	glBufferSubData(GL_ARRAY_BUFFER, state.last_item_index * sizeof(InstanceData), sizeof(InstanceData) * index, state.instance_data_array);
#else
	
	void *buffer = glMapBufferRange(GL_ARRAY_BUFFER, state.last_item_index * sizeof(InstanceData), index * sizeof(InstanceData), GL_MAP_WRITE_BIT | GL_MAP_UNSYNCHRONIZED_BIT);
	memcpy(buffer, state.instance_data_array, index * sizeof(InstanceData));
	glUnmapBuffer(GL_ARRAY_BUFFER);
#endif
	glDisable(GL_SCISSOR_TEST);
	current_clip = nullptr;
	GLES3::CanvasShaderData::BlendMode last_blend_mode = GLES3::CanvasShaderData::BLEND_MODE_MIX;
	Color last_blend_color;
	state.current_tex = RID();
	for (uint32_t i = 0; i <= state.current_batch_index; i++) {
		
		if (current_clip != state.canvas_instance_batches[i].clip) {
			current_clip = state.canvas_instance_batches[i].clip;
			if (current_clip) {
				glEnable(GL_SCISSOR_TEST);
				glScissor(current_clip->final_clip_rect.position.x, current_clip->final_clip_rect.position.y, current_clip->final_clip_rect.size.x, current_clip->final_clip_rect.size.y);
			} else {
				glDisable(GL_SCISSOR_TEST);
			}
		}
		GLES3::CanvasMaterialData *material_data = state.canvas_instance_batches[i].material_data;