That's one small step towards clarification, two distinct pairs of Samuel and Charlotte Knights. No obvious sign of a marriage for "our" Samuel and Charlotte.
On the other hand it increases the likelihood that Samuel and Emily are siblings with Lydia Knights, nee Palmer as the mother. The biological father is another matter: if Stephen Francis Bloom was Samuel's real father it begs the question of the Stephen Knights who is named as the father of Emily Knight's daughter Emily, baptised 1848.
If we are to believe the records Emily Knights of Hoxne was a spinster when her daughter Martha was born on 2 Jan 1837 (St Martin at Palace, bap 27 Feb 1837); her son Charles was the son of William Knights (at his first marriage) and had no father (second marriage); her daughter Emily had Stephen Knights for a father (bap 6 June 1847, St George Colegate); she died as the widow of John Knights (death cert) and was buried as an unmarried woman (cemetery register). Either there were 5 different Emilys, with only one visible in any census year, or the records are less than accurate.
To add another worm to the can - when Francis Stephen Bloom was baptised on 27 Apr 1828 his parents were named as Stephen and Lydia, late Francis, spinster. Her father was Francis Palmer, so presumably there was some confusion when someone asked her for his name.
The possible permutations are numerous - can only keep an open mind and carry on looking for more data.