Hi
On the BDM documentation you have, which you know is correct:
Your William ROSS b 1886 is the son of William ROSS, b abt 1858, a Cockenzie Fisherman and his wife, Jane (Jessie) MARSHALL. William ROSS (the father) b abt 1858 is himself the son of William ROSS & his wife Helen GREIG.
Census clearly show the couple, William & Helen ROSS - 1861 through to 1901 in Cockenzie. There can be little doubt this is your couple. There are no other contenders so likely to be the family of your William b 1858. Their ages are consistent with William born abt 1823 Tranent and Helen b abt 1821 Tranent - she being a year or two older than he. He is a Cockenzie Fisherman throughout. In 1851 prior to his marriage, he is living on his own in Cockenzie. In 1881, their son William age 22 is in their household, some months before his own December marriage to Jessie MARSHALL.
On the other hand the William ROSS/Joan HOGG line are Colliers - not Fishermen. In 1851 - their son William b abt 1838 is at age 13 already a Coal Miner, listed as born Gladsmuir, Haddington. I lose this William after 1851. He may have moved away?
All in all, it would appear the baptism Tom found "on 10 Sep 1821 of William Ross b 21 Aug 1821 Tranent Parish Church entry 16780, Parents were David Ross and Margaret Jonnes (sic)" is that of your William ROSS, future husband of Helen GREIG. The naming pattern evident in William & Helen's children support this.
The IGI shows issue to the couple (all extracted records)
Helen ROSS b 19 Jan 1856, Tranent - William ROSS & Helen GRIEG
David ROSS b 29 May 1857 Tranent - William ROSS & Helen GRIEG
William ROSS b 21 Dec 1858 Tranent - William ROSS & Helen GRIEG
Margaret ROSS b 14 Dec 1860 Tranent - William ROSS & Helen GRIEG
(double up with Tom's prior post - but I'll leave in here to illustrate my ' ideas' 
These 4 children are on the Census.
I can't see any reason why the 1853 parish record of the marriage of William ROSS the Cockenzie Fisherman and Helen GREIG the daughter of William GREIG, Cockenzie labourer is not yours? If they aren't yours, then we have a) the 1853 married couple disappearing after the marriage and b) no marriage for the couple who had the children! Seems unlikely to me - what was the reason your were told the 1853 marriage is not your couple's?
For argument's sake accepting the 1853 marriage
is your couple.....
.........since they married in Sep 1853, one would think there would be a child born earlier than Helen in Jan 1856. Possibly there was one around 1854 and this child died, maybe near birth but at least before 1861. Or perhaps Helen did not give birth to a live child before 1856 (miscarriage, etc) . Compound this with the fact any child born before 1855 was pre- civil registration and no such circa 1854 birth is found on the IGI for them. Many families only have their issue appear on the IGI after 1855 (often due to religion - ie: not established CofS, or because the parish records were not filmed/incomplete pre -1855).
In naming pattern:
If William ROSS (Helen's husband) was born 1821 son of David & Margaret - then William & Helen's first son should be "David" and 2nd daughter "Margaret". Their 3rd son, would normally be called "William" after William himself. However, his wife Helen, has a father named "William" too, so their 2nd son should be called "William". So far the pattern looks right.
Then we have daughter Helen born 1856 - the first born daughter we know of. Their first born daughter should be named after Helen's mother. Therefore, if daughter Helen b 1856 was their first born, then we might expect Helen ROSS nee GREIG to be the daughter of parents named William GREIG & Helen. Actually, because of the positioning of the known children - I'd have to guess
if there was a child born before Helen 1856, that the first child would have had to have been:
a) a boy named David (who died) and David b 1857 was named after him.
b) a girl named Helen (who died) and Helen b 1856 was named after her.
c) a girl named Margaret (who died) and Margaret b 1860 was named after her.
The latter c) would mean Helen's mother was also named Margaret (as well as William's mother, Margaret Jones).
So in summary - in my mind, Helen GREIG's mother is likley to be named either Helen or Margaret. The Scottish naming pattern is a tool, not always adhered to - but often is & is invaluable!
Tom has found a likely mother for Helen as Isabel - so that's interesting and upsets my theorising 
;D. Helen's death cert will be interesting to see....
Both William & Helen are still living in 1901.
SP has a death in Tranent 1903 : Helen ROSS other surname GREIG, age recorded as 81
Cheers
AMBLY
