Hi Joshua
I don't know how much you know about your David Thomas family, but I believe that David and his family lived in High Street, Abergwynfi, in 1901. The family are as follows:
David Thomas age 29, Collier, born in " Carm Lanelly"
Mary A age28 born in Pembrokeshire
Mary or May H age 4 born in Pembrokeshire
Lelian M? age 2 born in Pembrokeshire
They appear to be living with another family in 31 High Street Abergwynfi. So, as you have already stated, this family must have come to Abergwynfi within a few months of the 1901 census being take, as the youngest child, who is only 2, was born in Pembrokeshire.
I don't know if this is of any help, and my gut feeling is you already have this information, but just in case you don't, here it is.
And as you mentioned, you believe your ancestor was born in 1872, not 1862 as suggested in the Western Mail, by giving his age as 62 when he died. Therefore, the Neath entry would be the correct entry, as your ancestor died in Abergwynfi, so his death would have been registered in the Neath district