Two holes, one 1/2″ dia, the other 2″ dia won’t affect airflow or dirt entry much. Plug the 2″ hole with a plastic bung and make the hole for the hose a tight fit if you’re feeling particular.
As far as the length of the valve’s thread, that’s a valid concern. But honestly, you’ll never get ALL of the oil out of a motor — some will always be left. As long as you get 95%, it doesn’t really matter. If you want to, you can also measure the thickness of the pan metal and cut the valve threads to be the same length.
But a topsider has the same issue of not draining ALL of the oil.
The purpose of the valve isn’t to save time as much as save scut work. With the valve, you can drive up on ramps, stick the hose in an empty oil bottle, flip the handle and drain the oil into the bottle. No drips, no oily socket wrenches, no wiping an oil drain pan.