Hi Lisa,
I haven't solved your problem, but here are some thoughts / suggestions.
In the censuses Harriet is consistent about her age, which places her date
of birth about 1831. In 1871 she says she was born in Carmarthen, which
tallies with the baptism and in 1891 she simply gives Carmarthenshire.
However, in the 1851 census her place of birth is Pembrey.
If David Thomas is her uncle, it would be worth following him up to see
where he was born and if he had a brother Rees Thomas. It might be worth
following up on a link to Pembrey.
I agree that Rees Thomas and Mary Lewis were probably not married. But
Rees Thomas is stated to be a farmer on the baptism, not a ship's
carpenter. It is quite possible that Harriet made up her father's
occupation when she got married because she didn't know her parents / she
wasn't told. If Rees Thomas was a farmer he might have left a will. You can
see these online at National Library of Wales. If was a ship's carpenter,
you might find him in the merchant crew lists or naval records.
Have you looked at newspapers? I found some interesting articles at Welsh
Newspapers Online, which would be worth following up to confirm or
eliminate this Mary Lewis:
The Cambrian, 15 March 1834: At Carmarthen Spring Assizes Mary Lewis is
indicted for stealing at Carmarthen in October last [1833]. The crime took
place in Lammas St [her abode when Harriet was baptised]. She was found
guilty and sentenced to 7 years transportation.
The Welshman, 27 Feb 1835: Several payments are made in respect of Mary
Lewis, including for conveying her to his Majesty's ship "Hubberd" at
Woolwich.
Findmypast has come crime records, including some for Mary Lewis in 1834
[there are also some in the Carmarthen records, currently held at Swansea -
I have felons in my family tree]. FMP also has transportation records.
According to these Mary Lewis was transported on the ship "George Hibbert"
to Sydney, New South Wales.
If this is your Mary Lewis it would explain why she wasn't with Harriet.
I hope this helps. Denise