Workflow for email alerts on subfolders only

I've inherited a SharePoint site that includes sub-folders in the document libraries.

When a customer attempts to set an alert on a particular sub-folder, they wind up receiving alert emails for the entire document library. They have requested email workflows as a way around this, but I'm having trouble publishing a workflow that applies only to the sub-folder. The workflows will only publish at the library level.

Is there a way around this?

Even better would be to have a workflow at the site level that allows the email list to be defined whenever it is added to a certain sub-folder so that I can use an email with dynamic text across different libraries/sub-folders.