Mineral Resources
Gold? Silver? Diamonds? These were the main commodities that they traded their goods to the Europeans for, so you'd assume they'd be interested in the resources this region has to offer, in the long term.
How do they know they're there? As I said earlier, mineral resources only tend to be discovered after initial settlement.
Cash crops and subsistence crops
The climate's very similar to that of India; all of their major crops would grow there, along with plenty of potentially lucrative cash crops for the Indian market which actually are grown there today- sandalwood and indigo, for instance. And you could easily add opium to that list, if you want a crop to fill the niche of the tobacco plantations in the Thirteen Colonies.
Why would you sail all the way to Australia to grow cash crops you can grow at home and in the settled East Indies without the expense of extra shipping distance plus the costs of establishing plantations in virgin territory?
RE their food crop package- I do understand that rice etc are currently grown on the Top End, but I'd be interested to find out how much of this is assisted by modern farming methods. I think it's very telling that the Indonesians (though accomplished sailors and settlers) never bothered settling the Top End. They were aware of it's existence but no settlement. Of course this may have had nothing to do with the crop issue and more to do with the easy availability of large tracts of unsettled land in the Indonesian Archipelago (which, itself, means that it's a lot more likely to see added Indian settlement there as opposed to Australia)
Difficulty vs Incentive
In the short term though, kickstarting settlement in Northern Australia for an Indian maritime power shouldn't be any more challenging than it was for the British in South-East Australia, or indeed in Virginia in North America.
I agree. It wouldn't be any more difficult. That's not the issue.
You still haven't come up with a *reasonable* incentive to start a settler colony. Sometimes I think there's an attitude on this site that colonisation is somehow a (in the long term) easy process.
It isn't.
It's very expensive (both in lives and treasure) and creates huge administrative hassles. Europeans were incentivised to go exploring in order to find shorter, easier routes to Asia. Settlement of the Americas came after that and was initially spurred by the potential for cash crops and trade.
I'm wondering why any Indian polity (or private interests for that matter) would bother to go to the expense and hassle of setting up cash crop plantations when these crops can (A) be grown at home or (B) be grown in the East Indies which, assuming a South Indian thalassocracy scenario, are probably within their sphere of influence anyway. I just don't see an economic incentive.
Even where Europeans were concerned, settlement of Australia took quite a while to get underway- the coasts were generally mapped and ships would stop to get water and supplies from time to time but you don't see any foreign settlement until the First Fleet. The circumstances there were quite unique in that Britain had an established policy of transportation of criminals, had lost their previous preferred destination (the American colonies) and had a backlog of felons with nowhere to put them. Australia provided a temperate and (marginally) survivable destination (presumably they didn't just want to ship them off to the tropical islands to outright die like flies).
Solution: Something unique
I can understand if you want to (in your TL) put in something similar. Say you have an Indian maritime power that for various reasons doesn't want to settle its undesirables in Borneo or elsewhere in the Malay world (I'm not sure why- perhaps the fear that convicts settled there might conspire with rebels against the various Malay vassal monarchs of the Empire), then, ok, you might see settlements on the Top Side.
Or you could come up with some other, likewise, unique concatenation of circumstances. The favourite implausible one is "some prince loses a civil war and heads off into exile to found a new state". This doesn't usually happen- deposed princes tend not to like heading off into nowhere. You're more likely to find them either dead, glorified bandits, or at rival courts. But you get the idea- some sort of unique incentive for settlement.
But don't try to argue for an initial economic impetus, because there simply isn't one.