I have found details from the birth registrations of some of the children you mention, all registered with father Robert Thomas, mother Ann Jones and born at Llanerchymedd:
Ann - 30 Apr 1846; …..
I think it is very probable that Ann, eldest child of Robert Thomas and Ann Jones, is the mother of John Thomas - who was later renamed Owen.
Ann's baptism took place on 2 May 1846 (Llannerchymedd PR p43, 337), the address mentioned being Tai Club Mawr, Llannerchymedd, parish of Amlwch. In 1851 she is living in Wellington St. Amlwch with her mother's father Owen Jones and his wife Ann. In 1861 she may be a servant age 15 in Water St. Amlwch. I haven't found her in 1871.
thomasfamilyhistory mentioned that John/Owen's birth registration had the address Tai Club Mawr and the date, 21 Nov 1871, was almost identical to that in the 1939 register for Owen Thomas in St Helens (12 Nov 1871).
Robert Thomas and his wife had a son Owen b. 12 Oct 1864 who died 12 Jul 1865. It looks as if they became responsible for raising Ann's son John and chose to rename him Owen after their own son. (Calling Owen their nephew in 1881 was presumably meant to hide his illegitimacy).
I'll see if I can find what became of Ann after John/Owen's birth.