I've been doing a bit of reading on this as I've just bought an Aorus 1080 Ti as well. The main issue with the bios was that the original F3 version came with a stock power limit of 250W, whereas most oem overclocked cards shipped with default power limits closer to 300W. This is the main difference in the newer bios (F3P) as it comes with a default power limit of 300W. Both bios allow the card's power limit to go up to the same 375W maximum.There is also rumblings that this issue may have been exacerbated in early Aorus cards - perhaps the first batch of 1080 Ti chips Gigabyte received were a bit subpar. But this should be resolved by now. It was also alleged that Gigabyte may have been lacking in quality control on thermal paste application. But your temps should give that away as soon as you load the card. (Ie, the card shouldn't be hitting higher than mid-high 70s deg C at load, unless your case has very poor air circulation).
So if you already have F3P bios, then there's nothing to update to.
I highly doubt that flashing the bios voids your warranty as Gigabyte makes these bios available directly on their support page. Re-applying thermal paste, however, might.