I don't let it boil all the way off to the point of drying up and out. I also have a filter on my faucet - blame the S/O on that as she doesn't like drinking tap, so the water is filtered through charcoal and whatever else is in that filter first, then added to the pot, boiled and drained. I squeeze the water out myself.
It's not the filtered water that's the concern (I use distilled) but whatever the water pulls out of the cotton that you want to keep away from the cotton by not letting the water boil off and down. Anyway, if you're happy with your method....
