URL path settings not supporting more than one level
That's strange. If you edit the URL alias manually, it shouldn't be automatically changed unless you bulk delete and update your URL aliases in Pathauto.

Have you checked your Pathauto pattern settings (/admin/config/search/path/patterns) to see if there is something overriding your changes?

You said that you inherited the site. Are there any URL/path-related modules that your predecessor has enabled?