Pete, the stones under the floor at Alton Priors were obviously made to be accessible (by way of the trap doors) to people once they were inside the church. The stones must have formed part of a ceremony, a ceremony still deemed necessary by the local congregation - what do you think that ceremony might have been?
Alternatively, when the floor was re-laid, the Church authorities might have thought the stones were of some interest and should be made accessible but that doesn't seem to make much sense.