Brakes going soft after raising car?

Although air is not "in the system" normally, there is air between the cap and top of the fluid in the master cylinder. There is also a vent in the master cylinder cap. The cap is there only to keep fluid from spilling out, it's not an air tight system. That's not how it works. I do agree brake fluid does absorb moisture. But it's designed to. At least everything but DOT5. Were it not for fluid sloshin all over the place, you could throw the masted cylinder lid in the ditch and go.
Its air tight enough. Alcohol base fluid, will take on moisture.
Most master cylinder boots are designed to drop with the fluid,vent in cap is to allow air in above the boot, designed to work like a bellows.