Pete G said "My guess is that the stones were rediscovered when the floor was done and a friendly vicar decided to put the doors in as a way of attracting more people into the church."

That is my view too. The wooden floor is not very old and neither is the trapdoor. I would guess that both are less than 100 years old and do we know if the stones were visible any earlier?

If I can make two comparisons, then you can tear them to pieces:

Alton Priors church is built in an area thick with sarsen stones. It is impossible not to fall over them. So when they wanted to build a church, they had to make choices - 1 Build it somewhere else, 2 Clear all the sarsens away and then build on the cleared patch, 3 Give up clearing when they kept uncovering more sarsens and build the church on top of them 4 deliberately build over a pagan shrine to Christianise it (but why were these stones any more sacred to pagans than the hundreds lying around in the same field?)

Alphamstone church in Essex
Here you have a stone free landscape. Stones of any size bigger than gravel are extremely rare and consist of sarsen or puddingstone boulders and some flint nodules. It is reasonable to consider that such rare objects might have been considered magical or sacred. Perhaps they were fallen stars or thunderbolts from the gods! These boulders are erratics left behind when glaciers melted. It is unreasonable to suppose that a large group fell from the glacier in a circle. It is therefore reasonable to assume that they were brought from nearby stream beds by the hand of man and arranged in a circle. In contrast to stoney Alton Priors, the site for the church was chosen to be within the circle of the only stones present and not on the vast expanse of stoneless land all around. The church is also on a mound which is likely to be artificial. Is the mound and the stones the butchered and re-modelled remains of a long barrow perhaps? Long barrows are not common in this part of the world, but there is one with a Saxon intrusion burial not so far away on Therfield Heath on the Herts/Cambs border.

I would suggest that the sarsens were once regarded as special because of their rarity in Essex and that the church was placed within them as a conscious decision. It therefore seems to me highly probable that the Alphamstone church was built to Christianise a pagan religious site or tomb. The same thing may have occurred at Alton Priors, but is there any evidence to show that the stones there have been deliberately placed where they now lie? I submit that they are just some of the many erratics left where they fell and the church builders could find no stone free place to build upon.

Nothing of the foregoing is intended to diminish the status of special stones chosen to act as portals (magical or otherwise) in other churches. I just don't think that the case for Alton Priors has been made.