I see this family had at least three sons named Thomas.
1: Thomas 1837-1845, aged 4 1841 census
2: Thomas 1846-1847, died 1y 9m
3: Thomas 1849 - ???, aged 1 in 1851 census

Thomas number 4 appears aged 7 in 1861 and 18 in 1871. I have not found a corresponding batptism, but the ages do correspond with your missing Allen, baptized July 1853.

Given the persistance in using the name Thomas, I suspect Allen was known as Thomas to his parents but he chose to use his baptizmal name after the death of both parents.