NLS does not replace your DAW's channel summing engine; rather, the claim is that it's the minor differences in each channel's sound in a given desk that gives us the analog goodness that results when engineers use outboard summing boxes.
Waves modeled 32 individual channel circuits plus the master bus of each of the three desks. This may or may not result in the effect you're interested in; the only way to know for sure is to try it yourself.
You can mix and match different desks, use channel plugs or bus plugs by themselves, etc. There is a VCA-group function where a bus plugin can control a group of channel plugins, but that doesn't mean it actually sums their signals. It just enables you to change a group's settings (console type, drive, noise, etc.). IOW, there is no sidechaining of audio signals going from the channel plugs to the bus plug.
The closest thing I'm aware of in DAW-land to what you're describing is Studio One's "Mix FX" plugins, which are inserted in a special bus slot and can act at a lower mix-engine level than regular inserts. The only third-party plugin compatible with this so far is Softube Tape, but other parties are reportedly working on more. Should be interesting.
Cheers,
Eddie