Creating gerber layer for glue screen creation
It's completely possible in some EDA software to do this. For example, in Altium you can create a mechanical layer pair called something like 'glue' and the designed glue dots will appear on the appropriate layer for the component (top or bottom, wherever you put the component). So two Gerber files could be created and, say, if you only needed the glue on the bottom layer you could ignore the top layer. 

This would require that the person designing the component footprints has enough knowledge about the size of glue dot stencil orifice that is required for each component. 

I don't know if this is common practice- my guess is that it is used within some organizations, but more commonly done 'manually'.