The noise and sub go through the Amp just the same as the rest of it - the osc mixer is before the filter, which is before the VCA (which is controlled by the VCA envelope). All additional modulations will be affected as well.
Try it - it's nearly identical to using program volume, there are maybe some subtle differences dealing with velocity mapping and such, but it's quite effective, highly dynamic, and for stage purposes (e.g. balancing layers, fading one in and out, adjusting split ratio, etc) totally workable.
Since they can't add a knob for it as a firmware update, this works pretty darn good as a replacement option.