It's a little wonky in that the intended rest mechanic should be Hit Dice between battles; but I think it will make more sense once we see the "4E conversion" DMG kit, which I suspect makes short rest a 5 minute conversion.
That doesn't really answer the question at all. Whether the length of the short rest is 5 minutes or 1 hour, the point is that if you rest for [double the length of a short rest], you get twice as much benefit if you're jumped by a goblin halfway through.
Alternatively, if you rule that bonus actions can only happen during a fight, or that second wind may only be used in combat, that also fixes the issue.
That makes it even weirder. Now you've got a situation where someone is all beat-up, gets jumped by a goblin, and suddenly feels better.
In general, I think it's a bad idea to have abilities that can only be used "in combat," or that are triggered/reset by going "into combat." I prefer a more fluid approach where combat and noncombat can seamlessly blend into each other.
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