Target a final volume, after losses, that gives your desired volume into the fermenter. The wort contraction due to cooling will be constant, so it won't affect your process. If you lose, for example, 1.0 gal/hr, then you'd start with 13.0 gal before a 90 min boil to hit 11.0 gal post-chilling.
If you were to take a kettle gravity reading using hot wort, it would read ~4% low, but since there's no (practical) way to take a hot reading, it probably doesn't make sense to think of it that way. It's the gravity of the cooled wort that matters.