I can't answer you question but I have looked at the censuses, baptisms etc and can see your problem.
One thing I can suggest is to get the "letters of administration with will annexed" for Francis Thompson, with any luck it will mention his son Albert with enough detail for you to know whether it is your man.
Francis and Eliza were lodging in Cambridge in the 1861 census. He dropped dead suddenly in church in June 1862, as reported in detail in the Cambridge Chronicle and Journal of 28 June 1862.
Admin was granted to Eliza Newby widow of Cambridge. Francis's London address is also given and is the same as where the Wine Merchant was living in 1841 with son Albert etc.
Eliza Newby was the daughter of Francis and Eliza Thompson, bapt in London in 1809, and she was living in Cambridge in 1861, hence Francis visiting Cambridge.
The interesting thing is that she married William Newby at St Nicholas Brighton in 1830, so that does show that the wine merchant in London in the 1841census did indeed spend time in Brighton around 1830.
Personally I think that is good enough but hopefully the admin will clinch it.
THis all sounds very interesting and I think helps. I have a slight issue with Eliza Newby birth in St Bartholomew The Great in London on 17 Feb 1809 as it says she was born on 20 Nov 1808.
I have the following children for Francis and Elizabeth. They all show Francis to be a Wine Merchant and various address all match up. I know that Francis was a Wine Merchant as Albert's son was my grandfather and from his birth certificate it shows Albert as his father in the right place at the right time and I know from my father something of the family history. Alberts marriage Certficiate shows Francis Wine Merchant as his father. So, so far so good.
Children are Richard b 10 Jan 1806
Edward b 3 Nov 1808
Emma b 6 May 1811 all these 3 bapt at St Mary's Lambeth in 1813
Charles 1822 bapt Christchurch City of London
Albert 1828 Brighton
Two problems 1) Eliz Newby nee Thompson I have a record showing b 20 Nov 1808 bapt 17 Feb 1809 St Bartholomew The Great Church London this clashes with Edward
2) Also worried that I may not have the marriage for Francis and Elizabeth correct I think it is Elizabeth Bailey 30 Oct 1808 in St Andrew by the Wardrobe Church London although no mention of Wine Merchant only the banns. (Can you get a marriage Certificate for this early?)
I have also found a marriage in 30 October 1808 to Elizabeth Munt in St Saviour Southwark
21 February 1795 St Marylebone Westimster to and Elizabeth Dodd.
To say I am stuck and confused is an understatement.
Thank you for the piece on Cambridge that now makes a whole lot of sense and also I think Elizabeth must be right as that would make sense as to why they were in Brighton when Albert was born Also Newby comes up as a second name in one of Albert's Children's name. Any suggestions would be greatfully received