Also, Goa's existence was because it was so marginal. The Mughals, Marathas, and various regional kingdoms didn't care enough about the Portuguese, and also it was de facto treated as a factory (a free trade zone) - just like Surat was for the English
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To be fair, Dutch control of Java was more on paper than it was in reality. Most governance was devolved to local Rajahs who paid tribute to the VOC. Actual guns on the ground control across Java and most of what became Indonesia didn't really happen until the late 19th century
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> The Mughals, Marathas, and various regional kingdoms didn't care enough about the Portuguese
Sorry to be that guy, but Marathas cared deeply about Goa and they constantly waged wars against them and liberated most of the territory by 1739. Except tiny enclaves like Daman, Diu and Velha Goa most of the Provincia do Norte including the crown jewel of Baçaim (Vasai) was lost. Velha Goa, Anjidiva etc were saved by a stroke of luck due to the arrival of fresh Portuguese Armada with a new Viceroy.
The current boundaries of Goa were only extended later when the Rajas agreed to merge with Portuguese during Maratha civil war period on 1790s, however the Hindu elites retained most of the autonomy like the Visconde of Pernem.