It depends on what is used to make the butter the yellowish color. In America, for example, the annatto seed is used to color butter sold in the grocery stores and is what gives butter its yellowish color. It is also used to make cheddar cheese orange. The problems we run into here in America are the laws about whether a manufacturer is required to state that something has been added to the product or not. If an ingredient has already been added to the product when the manufacturer gets the food products he is using to make the final product, by law he is not required to list any ingredients he didn't add to the final product himself. Some people are actually not allergic to the actual dairy but are allergic to the annatto seed powder that is added to most commercial dairy products in supermarket shelves. And, most dairy products in America come from cows which have been fed a lot of hormones and an unnatural diet of corn and grain, instead of natural grasses and hay. Many products also have preservatives added to them. Not all are even required to be listed with the ingredients. So, you would want to be sure about what is required by law to be written in the list of ingredients in India and what is not required.
I have found that the fewer ingredients added to the final product the better. There is a much smaller chance of having to worry about an allergic reaction, for example. So long as the dairy is kept clean and the person making the homemade ghee is keeping the equipment clean and is following proper health codes and hygiene, I know a lot of people in America would love to have a much fresher and cleaner source for dairy products like butter or ghee than what is available to most of the population. I know the people who do find themselves allergic to annatto seeds would be thrilled to be able to get the fresher butter or ghee that doesn't have the ground up annatto seeds added to the products.
They both are saturated fats. The store brought ghee usually has a coloring in it that makes it yellow. Suggest using plant oils without Transfats, if available, in place of ghee for a healthier benefit.