I do not know how the Shearwater models the real world...Yes a timer would help. Or, set the computer for 100% O2, immerse it in 3 ft of water, then breath your O2. The computer will start a new dive but at least it will calculate new tissue loadings while you are on surface O2. The added pressure from the water shouldn't make any difference.
In the real world, increasing the ambient pressure while breathing pure oxygen "pushes away" the Nitrogen form your tissues much faster. This is the principle of hyperbaric oxygen treatment for DCS...
So, if the Shearwater models reality correctly, keeping the computer at some depth will cause it evaluating faster offgassing than what is really happening (as in reality you are not at such ambient pressure, you are still at atmospheric pressure).