To refer to the initial question, there's no general default power plane polarity, different CAD tools have their preferences.
Negative plane artwork has some details that normally reveals it's nature, e.g. an outline has to be included to isolate the plane from the board edge. There are also commonly used file name syntaxes that designate the different gerber layers. For this reasons, I don't remember a similar misunderstanding as described in your post, even with hasty and sometimes poorly specified prototype jobs.
But it's clearly suggested to add a describing file to the gerber data that includes a full stackup specification, layer description with gerber file names, substrate thickness, copper weights, surface finish, special process details.