Over-kneading paratha dough results in a tough and elastic dough that is difficult to roll out and produces a chewy, less flaky paratha.
Kneading develops the gluten in the flour. Gluten is a protein that provides structure and elasticity to dough. When you knead dough, the gluten strands align and strengthen. For paratha, we want a moderately developed gluten structure, enough to hold the dough together but not so much that it becomes overly elastic. Over-kneading leads to excessive gluten development, making the dough very tight and springy. This makes it hard to roll out thinly, as it constantly shrinks back. Furthermore, the resulting paratha will be tough and chewy instead of soft and flaky. The layers won't separate properly because the gluten is too strong.
To avoid over-kneading, knead the dough until it just comes together and is smooth, then let it rest for at least 30 minutes. This allows the gluten to relax, making the dough easier to handle and resulting in a softer paratha.