I understand Sikh/Hindu/Muslim in the same regiment were differentiated by the uniform and in different sub-units?
It's complicated.

That's something that changed over time and varied with the three presidencies, so it's hard to make general statements. After the Mutiny it was thought that mixing up of classes and castes was a good idea, but there was also a trend within the Bengal regiments* towards the "class-regiment" (which is as you describe - each company of the regiment being made up of a distinct homogeneous group). But there were also many regiments that were entirely homogeneous.
After the mutiny and as the century wore on, the prevailing view of the British was that the so-called "Martial Races" (the hardy ruffians of North West India and the frontier) were a far more desirable commodity as soldiers than the Hindustanis. So increasingly you find Sikhs, Dogras, Jats, Punjabi "Mussulmans", Gurkhas, Afridis and other northern races being recruited in the armies of all three presidencies, gradually replacing many of the Southern Indians (except as sappers, their expertise in that field was well-regarded) and often eventually changing their designation to reflect their new make-up.
*They were always very faith and caste-conscious. It's no coincidence that of the three armies it was the Bengal Army that mutinied, while the other two largely remained loyal. The attitude with the latter was that one's faith was "put in your knapsack" when you joined up, and you focused your loyalty on the regiment rather than your caste-clique.