Yes, the CE numbers are at specified depth. For example the EN14143 test for the JJ-CCR was at 40 and 100m. But the volume of CO2 injected into the loop was constant at 1.6lpm at 1ata.
The O2 and N2 molecules increase proportionately with depth. But if CO2 is completely scrubbed (not strictly true), then the only source for new molecules is metabolism, which only changes with workload, not depth. Your constant and stable production of CO2 molecules (at constant workload) at depth is now diluted by many more molecules of O2 and N2 from your gas supply, compressed by ambient pressure but supplied at constant volume.
The O2 and N2 molecules increase proportionately with depth. But if CO2 is completely scrubbed (not strictly true), then the only source for new molecules is metabolism, which only changes with workload, not depth. Your constant and stable production of CO2 molecules (at constant workload) at depth is now diluted by many more molecules of O2 and N2 from your gas supply, compressed by ambient pressure but supplied at constant volume.