Interesting bottle filling stuff.
I have a question about using a slightly different technique. What about filling the bottle with sanitizer and then putting your counter pressure filler on there and filling from the top port (the ring just below the stopper) with CO2, pushing all the sanitizer out through the wand/bottom port. Once it has blown all the sanitizer out and is just pushing CO2, turn the 3 way valve to beer and start filling in the beer. That would basically be the same technique used for a keg, just on a bottle scale. I think you could do it with that counter pressure filler and remove the need for a vacuum pump (for those of us that don't have a pump handy).
Edit: Thinking about it a bit more, the convex bottom of the bottle would mean you would get a little sanitizer stuck down around there that wouldn't blow out, though maybe that could be worked around. Maybe having a bent tube that goes to a bottom corner of the bottle and you just have to tip it to get all the sanitizer out.