One reason, a lot of times, compartments are isolated is to prevent the boat from flooding entirely. This is especially true on multihulls. For instance, my boat has two buoyancy tanks in the aft section, under the cockpit, and they have no bilge pumps... but then again, they're designed to be water tight and unless damaged shouldn't need them. The rudder stock on my boat comes up into a stern compartment that is completely isolated from the rest of the boat, and even if that compartment were to completely fill with water, would do little to change the attitude of the boat.
I would be cautious about drilling limber holes through water-tight partitions, since you need to do it properly to prevent the water from causing damage to the bulkhead or frame. If the bulkhead or frame is wood-cored, you really need to seal the hole with epoxy to prevent the wood from being damaged.
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You know what the first rule of sailing is? ...Love. You can learn all the math in the 'verse, but you take
a boat to the sea you don't love, she'll shake you off just as sure as the turning of the worlds. Love keeps
her going when she oughta fall down, tells you she's hurting 'fore she keens. Makes her a home.
—Cpt. Mal Reynolds, Serenity (edited)
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Still—DON'T READ THAT POST AGAIN.