That there is some Indian introgression into Aborigibal genomes is completely not surprising based on phenotypic characteristics of their faces as well as other aspects of their cultures like language. It was remarked upon by "previous simplistic pre-scientific" British settlers, who it turns out were quite right. Many other older theories have turned out to get support from the genetic evidence.
The study above argues convincingly for later contact though. There were probably several waves, theres other (disputed) circumstantial evidence for this. When we sequence more (if allowed) we will find richer picture as the OP alludes to.
