I think a big part of the difficulty here is that "motivation" is a very broad term, and people often mix up different aspects of it (both intentionally and unintentionally). It pretty much covers the "full stack" of goal-oriented behavior: everything from the neurological factors that balance action vs. inaction generally to the most abstract meta-goals toward which actions are ultimately directed. When people say they "lack motivation", the experience they're describing might involve any mixture of deficiency in the biological foundations of attention and behavior, lack of identifiable goals, or lack of belief/understanding in the connections between actions and goals. An aphorism like "discipline beats motivation" can't possibly come close to engaging that full spectrum, so even if there's value in the underlying idea, there will probably always be people who feel that someone saying it is misunderstanding or ignoring their difficulties.

Furthermore, I think what people are sometimes confronting when they discuss motivation is personal belief in markedly different goals than society promotes. In such cases they're not really expressing a lack of motivation generally, but rather frustration with a disconnect between the goals they actually believe in and the goals that they've been told to pursue (typically with according extrinsic reward/punishment). Telling such people that they just need to develop discipline is probably about as useful as telling atheists that they just need to go to church.