Im not sure. Ive had a similar question in the past reguarding crew spacing per compartment.
A quick "fix" (if you want to call it that), would be to change the fatigue model in the damage control compartment in the fatigue_coef section of the basic.cfg file and bunk your officer there. If its a positive number, just put a negative infront of it and they'll gain instead of lose fatigue. Although if realism is your aim, this isnt the thing to do.
EDIT:
Another thing you could try is change the submerged/surfaced fatiuge values for the engine compartment. You can for instance set the E motor compartment to have a certain fatigue drain on the surface when not in use, and submerged when in use. Likewise for the diesal engines, so theoriticaly i think you can say, make the diesals a rest area when submerged and E moters a rest area when surfaced. Although this is just theory, you can adjust it like that, but if it will work without a hitch is another matter.
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