This is a kinda "damned if ya do, damned if ya don't" situation. If the code automatically brought all the story information from one issue to its new clone, that'd be great—in the situations you outline. However, many (if not most) comics aren't like this. <i>Superman</I> #1 doesn't have the same creator/story lineup as <i>Superman</I> #2. So if it did copy the individual story information over, you'd have to painstakingly delete whatever <i>didn't</I> carry over from one issue to the next.
Since, on balance, there are probably more things <i>dissimilar</i> between issues, Chris has set it up so that you have to intentionally put in each and every storyline. Now, to help, he has made it so that you can clone characters and creators at the story level. So you can clone from part one in issue #127 to part two in issue #128, but you've got to at least add a blank story to issue 128 for that to be possible.