Is there a difference between paneer butter masala, matar paneer, malai kofta gravy?
Paneer butter masala, malai kofta gravy and matar paneer are part of the North Indian cuisine where the base is mostly the same with some minor variations (like excluding cumin seeds). 

So essentially, you have a common base gravy for sweeter dishes like these and then you have a spicier gravy for other dishes.
Many Indian cuisines have this pattern. For example, Gujarati cuisine will have red chili powder, turmeric, garlic-ginger, mustard seeds, cumin powder, fenugreek, cilantro and jaggery, etc. as a general base with some additions and subtractions of the vegetable ingredients. 
Similarly, you'll be able to find common base gravies across Indian recipes and cuisines. 

But, when you say:
"In addition - It seems to me that the same thing could be said about aloo gobi, chana masala, baingan bharta, and many other dishes - Basically the same frying of onions, ginger garlic paste and tomatoes, but with a different ingredient added at the end (for example eggplant for baingan bharta)."

You are making a generalization which is not necessarily true. These recipes can vary quite a bit based on regional tastes, specially baingan ka bharta. This dish is a signature dish and needs a seasoned hand to deliver it right.

So, you are right when you say there is a common pattern across recipes.
But certain dishes like aloo gobi will exist in different forms across the country. But rest assured malai kofta, paneer butter masala and matar paneer are only prepared in the North Indian style.