I'd say they were both the same Thomas, and I'd say the first 3 children were his and Margaret's ~ or he married a different Ann a bit earlier.
here's 1871 census
RG10/4970 Folio 16 Page 26
Thomas Stephenson  head m 32  Butcher   Easington
Ann Ap        "              wife  m 26                 Tynemouth
Emily           "               dau       9
Walter 
S      "              son       7
Thomas S      "               "         5
Ann H Stephenson    5 months
all children born Easington
birth reg for Walter 
Siddle Stephenson  Dec Qu 1863 Easington 10a 321
  "  for Ann Hunter Stephenson  Dec 1870 Easington 10a   413             
You'll only be certain if you buy some birth certificates to find mother's name, and then the marriage certs, the local registrar would check for known details before you buy the cert, to be sure they're the right ones.
Hope this helps,
Barbara