I am confused by your question and terminology. The **Solder Mask** is an insulating layer that is applied to the top and bottom layers of the PCB to cover the copper tracking and via annuli (but not cover the via holes) and to help prevent solder bridging between pads on footprints. The **Paste Mask** is used to mask off all except the PCB pads to which surface mount devices are to be mounted so that solder paste can be applied to them in a defined area and amount. Solder paste is not normally applied to vias unless they are being used in groups for high current and/or reducing thermal r distance for heat dissipation into one or more copper areas in the PCB. Through hole components are not reliably soldered by using solder paste so are normally assembled and soldered into the PCB as a separate process. The **Paste Mask** layer can also be used to generate a thin stainless steel **Stencil** which accurately aligned directly on top of the component side of the PCB and used like the screen in a screen printing process to quickly apply solder paste to a PCB. Two stencils are needed for double sided PCBs.

I don't think that's strictly true Andy.  PIH (Paste In Hole) is a well established process in industry, especially for large pin-out connectors, although I agree it's probably not something usually considered for home construction projects as this one appears to be,

Thanks for pointing that out Mike. I wasn't aware of that.

@andyfierman It became essential when we started to have to put surface mount components on the motherboards.  In the old days we used the press-fit connectors where you literally pushed the connector into the holes and the barbs both made the connection and held the connector tight. But if you then heat the board to solder the SMT components the connectors loosen a little.  Or if you solder the SMT components first then the forces involved in press-fitting the connectors often cracked the SMT components open. For a while we went back to wave soldering the connectors but you've always got the worry it will loosen (or even wash off) some SMT components, or if you do it first then soldering the SMT components could loosen the connectors.  So PIH became the preferred way.