My journey to trace the origins of South Indian religious worships has taken me to its tribal roots and not to that of Indus valley. The common deity of Indus valley people was goddess in idol format. I did not find any evidence of linga or yoni in Kerala, Tulu Nadu religious practices. The majority of Kerala temples are dedicated to Bhagavathi, a female goddess again in idol format.
But things are more complicated than this. Bhagavathi is a Devi(goddess) and not a Daiva(spirit). The real spirit goddess is Korati. However, she is not worshipped in Sthana(Bhagavathi temples). All the spirits and Naga(Serpent spirit) have their shrines outside the main Bhagavathi temple as these are considered low. Korati is considered a part of Bhagavathi. And Korati was worshipped in symbol format ( a rectangular wooden piece, a long sickle and something else that I forgot). So it is obvious that all the idol goddesses even in this region are in fact much later phenomenon. The worship of spirits and serpent by the non-tribals in fact show continuity of their tribal religious practices. I do not think even tribals along South-West of India worship linga and yoni. That is more or less North-East phenomenon.
In my opinion, any connection between South Indians and Indus valley could be found only in their deep common ancestry in Southern Central Asia, predating the period of Indus valley. When the Indus vally civilization flourishing, South Indians were still tribes and probably started their civilization independent of Indus valley.
Interestingly, Korati was the main deity of the matrilineal houses(Tharavadu) or illam houses. Only the female head of the family could enter the shrine and offer prayers; no male members and females of other Tharavadus were allowed inside. I believe like most of the Hindu purity-pollution beliefs, even the entry to sanctum sanctorum was a cheap and perverted copy and manipulation of old native matrilineal traditions.
My maternal grandmother