Why does my flour sifter have cup markings
Only a tiny amount of flour will fall through the grating before you start actively sifting; there is a reason there is an agitator and crank to help force the flour through.  I am sure the idea was that you could use the sifter as a measuring cup.

Of course, since most sifters are opaque and the markings are on the outside, it is difficult to get a good measurement.

In practice, these markings are essentially useless, and you are far better off using a proper measuring cup, or even better, a scale.

Personally, I am of the opinion that sifters are hard to clean, not useful for anything else, and in general a pain.  I use a simple sieve when I need to sift.