Galley warfare was overwhelmingly dominant in maritime South-East Asia. The strategic naval geography is very similar to Meditterainean conditions, and for similar reasons galleys were preferred over other kinds of ships. This remained true throughout the EU period. When Europeans arrived in the region, local shipbuilders adopted certain Mediterranean techniques. I think there's very strong grounds for making the sea around Indonesia an inland sea.
From 'Of Fortresses and Galleys The 1568 Acehnese Siege of Melaka, after a ContemporaryBird's-Eye View' by Pierre-Yves Manguin in Modern Asian Studies, Vol. 22, No. 3, Special Issue: Asian Studies in Honour ofProfessor Charles Boxer (1988), pp. 607-628:
“As is obvious from the drawing, the Acehnese fleet was constituted entirely of long, galley-type oared ships of various sizes.
The caption text says that altogether there were 300 sails, a somewhat smaller figure than that given in Couto's narrative of the siege (346 in all), in which he provides us with a precise list of the ships involved: 3 large galleys from Malabar, 3 'bastardas' galleys, 60 'fustas' and 'galeotas', more than 200 'lancharas' (malay lancaran), 80 'baloes' (malay balang), and 2 large 'champanas' (malay sampan) loaded with ammunition.
According to both Couto's description and our bird's-eye view (inaccurate only in the depicted amount of ships, not in the caption), we thus have a composite fleet, a mosaic of local and Mediterranean craft of various sizes. This is a typical situation for sixteenth and seventeenth centuries Southeast Asian seas. Earlier in the sixteenth century, Mediterranean shipbuilding techniques began to be introduced by the Portuguese and the Turks in the Indian Ocean. These soon spread into Southeast Asian waters, where they found a favourable ground for expansion, as 'long' oared vessels (as opposed to the 'round' tradingjong) had for many years been the backbone of local war fleets: they were well suited to the archipelagic environment of Insular Southeast Asia, with its small closed seas allowing for coastal navigation (cf. the Italian word costeggiare, often used for Mediterranean shipping) and frequently unstable winds.”