I was thinking about any contaminants in the air being left in the bottle, I just figured if I minimised that, it could only be agood thing.
Since I only boil the water and do not sterilize it in the autoclave (and since your beer will (usually) have a small level of contamination due to being sanitary and not sterile), it would be my assumption that there would be very few dust particles in the air, and that there would be fewer risks of contamination from that than filling the bottle with any liquid that is not sterile, anything in the air-space would settle very quickly and IMHO be no more risk - since the bottle is capped tightly - than filling it with liquid.
It seems that Coles does sell 'distilled water' but I wouldn't imagine it is sterile or even more sanitary than tap water, however the level of contaminants should be minimal, but boiling it or even better autoclaving it would be ideal - up to you if you want to be that pedantic.
Would you make any change to this process for WLP002? I find that it flocculates so well that I end up with lumps of (what I assume is) yeast, and they settle out first. Would you just throw them out with the trub and keep what's left in suspension? I guess you could also give the jar a good swirl to try to "dissolve" some of the lumps.
As
Fourstar said, I just shake the crap out of the jar in an effort to break up all the clumps and flocs, that way you should still get an adequate speration of layers, even if you do discard some of the most flocculant yeast that settles within a few mins.