I don't think the boil time affects gravity, does it? Mash temp/time would affect gravity but once the wort is in the boil I think it's set. I'm no expert so I may be wrong on this.
Been a while since I messed with my boil times (mines set to 90) but, I think it adjusts the ingredients and/or water needed to compensate and keep the gravity on target.
The OG estimate should be after bringing up to final volume before pitching yeast. The amount of sugar in your wort remains constant regardless of how much water there is, so the sugar concentration will only change based on the volume of the wort.