The Two nation theory says nothing about non-Muslims.....it says Indian Hindus and Muslims are two nations. Nowhere in its proposition does it say it applies anywhere outside of the Indian subcontinent...and nowhere does it say anything about religions other than Hinduism and Islam.
Offcourse it will say about hindus when we were talking about partitioning India: a hindu majority nation. Why it need to talk about religions not in question? But from where it inherit this argument? Isn't it kafir vs non kafir divide? Us vs them divide? True religion vs Wrong religion divide?
Are jews and muslims same nation? Are atheist and muslim same nation? Are christian and muslim same nation? Jain and muslim same nation?
For which other religion, muslims are flexible to and can adjust their way of living and sacrifice their own, unless muslims are minorities?
If two nation theory talks only about hindu vs muslims, can an Ahmadi/sikh/christian be the head of Pakistan?