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To prevent them from showing through the floor, there's the chance that either the gap between countersunk screw head and floor will show once it's been walked on a bit (or glued down etc.) or that the screw head will be slightly proud (in which case filling will show it up). I guess movement or swelling would be a secondary consideration, especially since it's always worth figuring a flood of some small type every 10 years of occupation, accidents do happen!
How come?
To prevent them moving up over time with temperature / humidity changes in the ply? Or so there is no "low" spot?