When you consider India's population, especially the working populations who migrate to these cities in search of jobs/education, etc., there aren't enough to sustain the pressure, and there aren't enough resources to support such a large crowd.
As evidenced by the conditions in these cities, the majority of them are either saturated or on the verge of saturation. As a result, the government must establish a new center for businesses, corporations, and so on. Opening a government institution such as IIT or IIM leads to an increase in business, at least locally, and later attracts investments from major market players such as real estate developers, malls, health care providers, and corporations, eventually leading to the industrialization or urbanization of cities.
To lessen the strain that these cities would otherwise face from having to support a new IIM or IIT, which would once more increase in-migration and intensify the city's problems. This could be one of the good reasons for this. So, establishing such institutions in these cities is, if not a good idea, a better idea. Many may contend that this represents a significant setback for some batches graduating from such Institutions at this stage of development.