Not really "self contradictory" at all. There was an intermediary population living on the ruins of Harappa, regarded to be more agrarian than the city builders of the antecedent intact IVC. This itself likely constituted a combination of migrants from multiple origin points and also some of the original Iranics of the IVC itself.
In fact, the Rakhigiri data in Shinde's paper CONFIRMS this, rather than refuting it. The Rakhigiri specimen is from 2500-2000 BCE, the mature phase of the IVC. Collapse of the IVC began in 1900 BCE. Just when exactly are you postulating that "Aryan DNA" sneaked into the genome of the IVC if it WAS NOT THERE 100 years before the collapse of the IVC? If you bother to read the paper, it is even speculated that the female specimen may have been fleeing from other IVC sites due to climate effects.
It is your own researcher Shinde who actually REFUTES "Out of India" theory comprehensively, the more you read the works in question! It is duly confirmed, to anyone reading the data without Saffronised spectacles on, that (a) the Aryans (and whatever they brought with them) were foreign, and (b) the IVC itself was Iranic origin, and (c) NO substantive Aryan genomic influence existed in populations inhabiting Harappa until after the collapse of the IVC.
Modern genetic compositions for reference: