The red Extra Reserve slots are technically the torpedoes stored in the bilges under the floor plates in bow compartments.
In game, I think it only really matters if you're using h.sie's and Stiebler's patches and resupplying at sea.
In reality, its only affected the VIIs. They had to carry electric torpedoes (G7e) in this location because the supports could damage the G7a engine. The opposite was true for the aft reserve torpedo; there was no access for battery maintenance for G7e's.
The XIs (from what my research has shown) had no restrictions aside from external storage.
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