Well this is a bit of a long shot.
The marriage cert suggests he is illegitimate.
In 1891 there is a household with a Joseph Lewis and wife Gwenllian plus son Joseph D lewis aged 1.
There is this marriage
Sep 1890
Anthony John Swansea 11a 1271
Griffiths Gwenllian Swansea 11a 1271
LEWIS Joseph Swansea 11a 1271
Richards William Henry Swansea 11a 1271
Thomas Mary Hannah Swansea 11a 1271
So, maybe Joseph was registered under mother's maiden name and then mum married?
Barbara