Asking what the rationale is, you're not going to get an answer here. That's something only the FCPX dev team would know, as we all know. But asking what our personal opinions are on the issue, is a reasonable question to ask on a forum.
Replace commands are replace commands, not overwrite commands.
Connected clips do not have the characteristics of Storylines; no magnetic functioning, no transitions, etc. If you want Storyline behavior, you need to make a Storyline. Makes sense to me, personally. As for those connected clips, Replace commands work or me just fine (Replace, ...From Start, ...From End). The differences between connected clips and storylines works for me, I can use one or the other, pretty simple to understand IMHO. Just like Sync Clips and Multicam Clips don't work exactly the same.
Again, this thread is going to be personal opinions and speculation about what happens at Apple. Which is fine.