Can someone explain the logic behind infantry without a save getting a 6+ "cover save" when the vehicle they are INSIDE gets destroyed?! Surely any protection offered inside a vehicle is somewhat negated by said vehicle getting obliterated!

The vehicle isn't neccesarily blown up. Maybe the tracks are blown off an it is imobilised.

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Epic: Hive Development Thread

In epic units become casualties, not dead per say. So yes, immobilised, crashed, buried, part destroyed, blown up after the ammo cooks off etc.

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Yep, over 80% of AFVs "knocked out" are repairable ... Catastrophic destruction is rare ... Unless an AFV is burning, blowing up, etc. it will provide some cover/concealment.  

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If a Vehicle is "destroyed" by a Macro Weapon the transported troops would be classed as being hit by a Macro Weapon too and would only get a save if they would normally get one if hit by a MW.

You could also refuse to take any saves on your transported troops that had a chance of survival if it bothers you that much,just don't be unsporting and expect opponents to do it.