There is one other family of Owen & Maria Jones in the 1891 census but they do not have a son John Thomas.
1891 census
RG12/2936 folio 104 page 33
48, Bilson St. Toxteth Park, Lancs
Owen Jones age 45 Tailor b Anglesey
Maris wife age 45 b Flintshire
Moses son age 19 Tailor's ...?.. b Liverpool
William son age 17 Taveller b ditto
Margaret dau age 15 Dressmaker b ditto
Jane dau age 12 b ditto
Lilly dau age 4 b ditto
This family were also in the 1901 census
Rg13/3440 folio 30 page 13
Owen Jones age 56 Tailor b Anglesey
Maris wife age 56 b conway
Margaret dau age 26 Dressmaker b Liverpool
Mary dau age 14 b ditto
1891 census
RG12/30255 folio 147 page 31
96 Junction Lane , Sutton, Lancs
Owen Jones age 28 Coal Miner b Wales
Mary wife age 30 b Holyhead
William son age 13 b Bethseda, Wales
Robert son age 12 b ditto
Elizabeth dau age 9 b ditto
John Thomas son age 5 b ditto
Margaret dau age 2 b ditto
David son age 1 mth b ditto
could not find this family in the 1901
Hope this helps
Meliora