You contradicting yourself by stating that the Vedic culture and the IVC culture developed in different eras.
Pagan elements were included in Judaism because the people were the same that went from Canaanite paganism to Judaic monotheism. Similarly, Christianity developed among Jews, Islam among Arabic pagans and Christians, incorporating elements of both.
Using these examples prove that either there was ethnic continuity or direct interaction and cultural exchange.
The differing levels of genetic integration in the subcontinent actually points to both being true.
The dots in the Swastika were a recent addition. Old swastikas in the Aryan period did not have them either. In fact, for a long time, traditional Hindus were reluctant to include the fourth Veda, so that explanation for the four dots does not even work. Here are perfectly Hindu Swastikas that do not possess any dots.
Just as Judaism adopted elements of Paganism, then Christianity adopted Judaism, and finally Islam adopted elements of Christianity, the Vedic period (precursor to Hinduism) adopted some elements of previous civilisations, like the IVC.
This doesn't mean they were modern Hindus with the same widespread rituals and traditions they have today.
Vedas were composed after the gradual decline of the IVC, and since both civilisations regionally existed next to each other (but in different eras), the Vedic culture borrowed some elements from the IVC, which came before.
It was not the other way around, nor does it prove that the Vedas were composed during the mature Harappan period and that these symbols held the same meaning for the people of the IVC as it does for Hindus today.
The Swastika seal you posted also lacks four dots that are widely used by Hindus today, often symbolising the four Vedas (Rig, Yajur, Sama, Atharva).
They didn't exist during the mature IVC period, hence these dots are not present in old Swastika seals.