The panspermia hypothesis has the same problem with the early Earth's environment as the native origin theory does, though. If Earth during the late bombardment period is too hostile for life to begin here, why is it somehow more benign for organisms coming in from outside (which have the added difficulty of making it in through the atmosphere without being quick-fried to a crackly crunch).
It doesn't necessarily need to be organisms coming in on comets. It could just be complex compounds. The point is, somehow those complex compounds were around earlier than they ought to have been and we don't know why.