Well because the seal made by the cap to the bottle is not as airtight as what your brake system is, plus depending on how much you use up there is more air content in the partially used up bottle, than what is in your reservoir of your brake system.
your reservoir has a rubber seal, the cap on the bottle does not
by the time I wear out a set of pads, I will replace them, along with a full flush of the lines, so I really never have that much left over, and what is, is used just in case and after that it gets thrown out, next pad change and line flush a new bottle is purchased