I'm not sure I understand your question. Seems everyone does this type of thing differently. If you have a MFG app note that makes a suggestion, that's likely how you should do it, which is likely different than how many people would do it. Do you mean a pattern like this.
padinvia.jpg
The above pattern would help guarantee you have a certain amount of solder contact, but also guarantees you will have a specific amount of no solder. This would be very difficult for the solder paste plate, as there is no supporting material for those little pads. Also you have to control your mask thickness, it's common that you get a .003 thick mask, but often the mask is .0005 thick. If you don't control your mask and paste thickness close enough, you can easily cause the chip to float. Your solder past is typically between .004 and .007, if you chew up .003 in your mask, you can cause floating problems with not having enough paste to catch the flying leads. You need to first specify the specs, then the MFG needs to build to the spec instead of standard processes often used by low cost MFG's, and if you have a problem you need to have inspection equipment which allows you to prove the MFG didn't follow the spec. It's a difficult way to MFG things. See mask dry film thickness noted in this link
http://www.multilayer.com/pdf/ManufacturingCapabilities.pdf
Perhaps you mean a pattern like this.
QFN-Paste-1.jpg
This is a more common approach. This pattern allows a certain amount of out gassing during re-flow, and generally allows you to fill the majority of the chips thermal slug. The concerns about voids is usually addressed by having a low humidity in your paste, and using a paste with flux that has minimal out gassing. If you don't have proper humidity controls, the boiling trapped gasses usually pop the chip off the board like a piece of popcorn. If your MFG properly controls those two parameters you generally don't have issues with voids under your chips. As well when you let excessive solder to flow into the via's, it prevents the floating issues.
I think you are inquiring about the top picture with lots of masked holes. For that pattern I would likely create a flood on the paste layer that matches the suggested slug area, this allows you to specify the mask clearances which would then make the holes in middle.
If you mean like the bottom picture, I would add those paste pads in the footprint.
I'm not sure there's a real proper solution, as long as you get the pads where you want them, and you get them there efficiently, you have succeeded.
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