The idea is that all your accounting data including attachment is self-contained within single .manager file which can easily backup, transfer etc.
There is a value in keeping things simple and self-contained rather than having your attachments scattered all over the place. Maybe your use-case is simple. Just invoices for single business. But Manager has many types of documents which can contain attachments and then most users run multiple businesses. You can see how complexity can quickly explode when single folder can have sub-folders (for each business), then sub-subfolders (for each transaction type) and sub-sub-subfolders for each transaction (because one transaction can have multiple attachments) etc.