1) On most Handcannons, I think you're looking at the wrong barrel. The top tube, which seems to be in alignment with the cylinder, is where the flash comes from on most of them. So I think the entire system is designed correctly. The hammer height is possibly more due to design/aesthetic choices, or for easier cocking.
2) MGs might be using a feed tray to shuck the rounds from the belt and drop them into the barrel, this the elevated position of the belt. Or possibly, the belt physically feeds downward into the barrel when the gun is cocked.
3) On Scout rifles, I think the rounds are feeding upward through the rear of the gun, by the stock. They then are grabbed by the chamber sliding back, loaded as it slides forward.
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