Hmm. Maybe, maybe. After all, researchers have found Polynesian DNA in the remains of the Native American Botocudo, a tribal group that originally lived in South-East Brazil, on the Atlantic coast, which was violent and independent, didn't come under the control of the Portuguese colonials, and got wiped out for that reason before the end of the 19th century. Even the researchers themselves are still at a loss to try and explain it without admitting that Polynesians could well have transversed the Andes and travelled across South America, or that they could have sailed around Tierra Del Fuego and into the Atlantic. So then, if you counted the Botocudo as an Austronesian group, and went with the Polynesian settler origin theory instead of the escaped Polynesian slaves origin theory, then you could simply have the Botocudo, or their original predecessors, retain their maritime tradition and venture across the Atlantic; with these Austronesian-descended settlers establishing settlements on the then-uninhabited islands of Cape Verde, the Canary Islands and the Azores. Would that work?
EDIT- or, alternately, you could have Malagasy Austronesians sail around the Cape of Good Hope and settle some of those islands, like Cape Verde and Sao Tome et Principe, themselves. But then, you wouldn't technically have them crossing the Atlantic to do so, would you? And sure, these settlers could then easily cross the Atlantic from those outposts, but fulfilling the challenge this way would require two stages of colonization and settlement, and require markedly more time (albeit with more time available, given the arrival of Austronesian settlers in Madagascar i.r.o 350BCE>550CE, perhaps a thousand years or more before the Polynesians could possibly have got to the Atlantic in the Americas- giving them far more time to push on into, and eventually across, the Atlantic from there).