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Hi,
Maybe I can help a bit. Most of the information which follows comes from transcriptions of Anglesey BMD certificates and some does not fit with information you already have.

There is a birth registration for Elwyn son of William Williams and Maggie Ann Jones b. 12 Jun 1942, Llanddeusant.
Marriage 7 Nov 1936, Holyhead Registry Office - William Williams, 20, b, agricultural labourer, Cae Bach, Llanddeusant, son of Owen John Williams, farmer and Maggie Ann Jones, 20, s, Penbonc, Llanfugail, dau. of Thomas Jones, agricultural labourer.
I can find birth registration for two of Elwyn's siblings - Llewelyn and Jean.

Deaths registered on Anglesey in 1986/7 for William Williams (no middle name):
17 May 1986 age 63; d.o.b. (from FreeBMD) - 5 Apr 1923
28 Jun 1986 age 85; d.o.b. 18 Feb 1901
19 Sep 1987 age 78; d.o.b. 8 Apr 1909
Note none of these were 20 in 1936.

Birth registration:
William son of Owen John Williams and Jane Thomas 26 Aug 1916, Llanddeusant.
Using this d.o.b. it seems that William Williams' death was registered in Birkenhead:
1987 Birkenhead 37,672, d.o.b. 26AU1916 - on FreeBMD.

If you think this is correct let me know what further information you need.

Many thanks for all replies - very helpful.

DebNZ: Given what follows it seems 'my' Anne is different.

cupoflife: The marriage to John Goodwin in 1858 and the birth of Robert Goodwin in 1866 could well refer to 'my' Anne Phillips. Could there be any supporting evidence available other than through buying copy certificates? Where does the marriage date - 20/10/1858 - come from?

Debra/Dundee: From Victoria records I see that John Goodwin died in 1873 aged 38, he was born FLIN (which means?) and his father was Edward. Very helpfully it gives his spouse as Ann Phillips.
Anne Goodwin then marries Alfred Quinton in Victoria in 1874. (No other details)
Ann Quinton died Melb Hosp in 1884 age 48. Her father's name of Robert Phillips is useful supporting evidence.
Find a Grave does not seem to have any of these burials.

Sadly, there is a death (6587/1874) of Robert Goodwin age 8 in Victoria records. He has father John and mother Ann Phillips.

Google Books has a copy of "I am a Government Man to Mr Scott of Glendon - Hugh Hughes: From Convict to Free Man" by David Cragg (2015, Australia) which details Hugh Hughes' full story - the theft of the two horses, his flight from Anglesey, the arrest, trial and transportation to New South Wales. The final approx. 170 pages describes his life in Australia. But the book has little to say about Hugh Hughes' family, only that he was born on Anglesey in 1804 to Hugh Hughes, farmer and his wife Margaret nee Prytherick (i.e. Prytherch or Prydderch) and that he was a cousin of William Prytherick of Ty Mawr, Llantrisant, the owner of one of the stolen horses.

As mentioned by Tall Al above patronymic naming was common in rural areas of Anglesey in the early 19th century so we cannot assume that Hugh Hughes' father had surname Hughes.
Prytherch is a much rarer name than Hughes so I've looked for information on his mother Margaret Prytherch.

There was a marriage 18 Dec 1804 at Llangristiolus between Hugh Prichard (Prichd.) and Margaret Prydderch, both otp and ipo Hugh Prytherch and John Knowles.
Then Hugh, son of Hugh & Margaret Prichard of Tyddyn Isaf was baptised at Llangristiolus, 10 Feb 1805. I think this may be the Hugh Hughes we are discussing.

These are the baptisms of some of Hugh's siblings:
Richard, 8 Nov 1807, Llangristiolus - son of Hugh Prichard & Margt his wife.
Anne, 15 Nov 1812, Llangefni - dau. of Hugh Prichd of the parish of Llangristiolus by Margt his wife.
John, 23 Apr 1815, Llangristiolus - son of Hugh & Margaret Prichard, Tyddyn Isaf, farmer.
Mary, 20 Apr 1817, Llangristiolu - dau. of Hugh & Margaret Prichard, Tyddyn Isaf, labourer.
Richard, 23 Apr 1820, Llangristiolus - son of Hugh & Margaret Prichard, Tyddyn Isaf, farmer.
Robert, 12 Mar 1824, Llangristiolus - son of Hugh & Margaret Prichard, late of Tyddyn Isaf now of Llangefni, carrier.

In the 1841 census Hugh and Margaret Prichard, both aged 60, and their son John are at Glan Hwfa St. Llangefni, together with Jane and Margaret, both 30, who may be two other daughters. Hugh is descibed as a coal carrier.

I'm not sure that this is all convincing, but maybe it helps?

I haven't found a suitable marriage on Anglesey for Ann Owen/John Thomas either but there is a civil/non-conformist marriage in the Bangor district (O,N,D qtr 1883 Bangor 11b, 888) which could be them.
By the way I think the Richard Thomas you mention from the 1901 census in Liverpool is a brother to John Hugh Thomas, so uncle rather than brother to Owen Hugh Thomas. Richard was born 6 Nov 1867, Llangefni to Hugh Thomas & Ellen Jones.

I looked at this family when I was trying to understand a DNA match I have (with a descendant of Mary Ellen Thomas, Owen Hugh's half sister). I didn't find the connection.

I suspect he was not the father as he is not mentioned on the certificate. And because the mother subsequently had a number of children with a second man. The first child believed the second man was his father until he saw a copy of his birth certificate.