David, I replaced my outboard with inboard diesel some years ago but decided not to fill in the base of the well and to keep the removable 'plug' which fills it in. This meant a rather shorter skeg but it means that I can remove the 'plug' and clear the prop from inside the boat should I need to.So, with the 'plug' in place, I have exactly what you are proposing ... i.e. a 'leaky' well with a few small holes in it. This allows, as you say, the well to fill up to the waterline.There are absolutely no problems with this.The water moves around surprisingly little in the well when moving fast but going out as fast as it comes in by the same venturi effect.It does mean that I also have a very rapid cockpit draining system!
Chris. Elsa SS26 103