I agree the current layout of saved searches isn’t the best. I’ve tried some alternatives (such as a different group), but wasn’t too excited about those either.
One constraint is that (at moment anyway) I would like “Home” at the top and everything else indented under “Home”. When searches are in their own group it becomes less clear I think that you can clear the search and see everything by clicking home.
Anyway, I still don’t think I’ve found a final solution. But in this next release I’ve changed the UI a bit, in the sidebar. Hope to release that later today, then please let me know what you think.