Who is responsible for panelizing solder paste layers?
I do not know what the industry standard is, but we order our paste stencils from the same manufacturer who makes our bare PC boards.

We allow the PCB manufacturer to have some leeway in how the boards are panelized.  Because it is them who decides on the board spacing in the panel, it simply made sense to have them manufacture the paste stencils as well.  The fact that they give us an awesome price for the stencils when ordered at the same time as the PCBs doesn't hurt either.

We then take the final specifications (array arrangement and spacing) from the manufacturer to generate the PnP files.  For our little bitty machine (prototyping), the PnP file has one copy of the PnP information plus array arrangement and spacing for the remaining boards in the panel.  

I'm guessing that our CM does things similarly - we send them our PnP file as generated by our CAD software plus the same array arrangement and spacing information.