Remember the VERY OLDEST rocks in the world , zircon crystles, are found on or near the surface in Austrailia. Also remember that the geologic column isn't nearly as uniform as you suggest. I have seen supposedly millions of years old fossils of dinos taken from 30 foot of mud in the Trinity river bottom. In Dino National Park they have heavely scrambled dinos with no fossilation of the plants that the dino ate. Some reason for the geological column are.
How objects (including living, or once-living, bodies) sink through water is determined by a variety of characteristics of said objects. Denser objects tend to sink faster than less-dense ones (which may even stay on the surface, depending on how light they are); objects with smoother surfaces, hence less drag, tend to sink faster than objects with rougher surfaces, hence more drag; streamlined objects tend to sink faster than objects with ungainly protrusions; and so on.
In short: The quicker a life-form's body sinks, the deeper its specimens will be found in the geologic column.
The Earth is not a perfect sphere; some points of its surface are higher above 'sea level' than others. Environmental conditions vary for a number of reasons, and altitude is one of those reasons. Since any one life-form generally prefers a particular set of environmental conditions, it follows that life-forms will tend to live at a particular altitude.
In short: Creatures that lived at low altitudes will be found, in the geologic column, below creatures that lived at high altitudes.
When the Floodwaters rose, all animals would naturally have attempted to escape their doom by fleeing to higher ground. This would have been a futile effort, since the Flood drowned all Earthly life except what was saved on Noah's ark, but some animals would have avoided their inevitable deaths longer than others.
In short: Creatures with greater mobility will be found higher in the geologic column than creatures with low mobility.
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