I've seen this happen with my ancestors, quite often the local church recorded their births and then the nearest largest town also recorded their births.
"Toynton All Saints is a village and civil parish in the East Lindsey district of Lincolnshire, England, about 1.5 miles (2.4 km) south of the town of Spilsby"
I think you are right Spilsby would be where they were officially registered at birth. In reality the actual physical birth was probably at Toynton.