How do internal martial arts work?

One way to explain it is that they improve alignment and thus improve the efficient transfer of force through the body. Alignment, in this sense, is not static alignment, it is functional alignment while in motion.

This type of 'improvement' involves moving in a smaller range. Internal martial artsKuo Lienying measure 'range' in many different ways, but for the sake of example we can simply think of 'joint range.' When we use a smaller joint range we do it because we are looking for that percentage of joint movement which is most efficient at force transfer. We then practice movement routines which use that smaller range until they become integrated or familiar.
Perhaps surprisingly, what happens when we do this practice is that we feel vulnerable. When we move outside of our efficient range, we notice the potential for misalignment or even injury. The more actual potential to transfer force one develops, the weaker, and more vulnerable one feels.

This is not the weakness one associates with being sick, over worked, or deficient. It is the weakness we associate with sensitivity and adaptability. I posit that all increases in power are do in some part to a reduction in range of movement while in motion.

As students improve they often exclaim something to the effect of, "I'm completely unstable on my ankles!"