I have seen the Cowling/Davies connection repeated on several trees on Rootsweb World connect but no details of the marriage - just a vague Cornwall circa 1823. Nothing shows up on the Cornwall OPC site. One tree shows William as William Floyd Cowling born 21 Dec 1838. The birth of a William Cowling was registered in Llandovery in March 1939 which supports your birth certificate theory.
Another tree gives the death of Thomas as 20 March 1860, with a calculated year of birth as 1802. IF this is anything like correct it does allow for Thomas Cowling(Mary Tavy 1805) son of Thomas to theoretically come into the reckoning. A father /son link seems more likely than some more remote relationship.
If he survived, Thomas would have been no more than 2 when the family moved to Wales. Perhaps, in later life hearing stories of the life of his father in St Agnes he assumed that this was where he was born. The details of 1841 are just about within tolerable limits but I have no explanation for his age recorded in 1851.
The first three children of Thomas and Jane were named Thomas, Jane and Philip. Philip was the name shared by the grandfather and brother of Thomas of Mary Tavy. It seems to me that this relatively uncommon name would more likely have been chosen from family precedent rather than randomly , particularly so early in the marriage. Later children carried the names of paternal and maternal grandmothers.
All this is highly speculative and I am aware of flaws in the rationale but I feel, on balance, that the younger Thomas was Thomas, bapt 20 Jan 1805, Mary Tavy, son of Thomas and Joanna. I don't think I'm likely to get any closer than that and, subject to any observation you may have, will record it as "possible"
