About modifiers applied to 3d groups, I just re-read the discussion we had on our internal issue system and here was the conclusion we made:
For 3d groups, it sounds very delicate to implement: when you have a 3d group, it means a collection of objects that can be displayed on screen. Smode does not know anymore how this object are constructed at this point. Having modifiers on top of 3d groups would have a very special meaning telling something such as "stack an instance of this modifier on top of each 3d generator you cross inside the scope of the 3d group". Sounds like a rather complex behavior, both on dev-side and on user-side in my opinion.
However, there is this closely related techniques that brings us one step farther: the Group Generators command enables to group multiple "3d generators" into a single one and then to display / apply effects on the grouped geometry.
Step1: do a multiple selection of 3d layers, right click > Group Generators:
Select one of the 3d layers as being the reference for modifiers and renderers:
Here we go, it becomes a single 3d layer on which you can apply global modifiers:
Nice, but those not solve the fractured geometry problem. I still have to take time to fully watch the video, but sounds like if we had a "group id" 3d mask consisting of discrete values that are constant along whole sub-objects, e.g. 0% (for the first sub-object) 10% (for second one), 20%, ... 100% (for the last sub-objects), we could with the help of a "function 3d mask" apply a given modifiers to different levels to each sub-object. Not sure it's clear, but there might be clever feature to implement there 
