Thank you everyone for your assistance.
I have just learnt that he was born in Madras, so I believe this is the Thomas born to Thomas Duckworth and Sarah Boot in 1837. Thomas' father marries Caroline Fuller in 1845 after first wife Sarah died, and the arrival record for the Palmyra in 1854 mentions that his mother is Caroline.
I'm fairly confident this is my ancestor now. The only discrepancy is that his mother is recorded on both his marriage and death certificate as Ellen Davis. I can't think of a reason he would make up a name (Sarah died when he was 6yo, but I assume he would still know her name). Thomas' wife from Australia was also named Ellen, but that's probably just coincidence.
Thanks again everyone