Th main purpose of topography is to represent ground level around a site (imported from survey data) so you can develop built environment site levels. You can't really have a hollow in topography because topography has a very specific meaning, it's top or it's not.
However (being self contradictory) I like the soil layers idea. From bore hole logs we should be able to plot and extrapolate between points. Geological features rarely have abrupt changes within the scale of your average site model. Probably at each point there should be the option for further lower levels.
I think there is room for improvement in terms of how pads could be allowed to overlap. Why not just say the lower of the two takes precedence in being a cut rather than the one over it being a fill (for the bottom one to exist it has to be a cut first). Also tagging support for these topo items was quite poor (non-existant) last time I used them, not sure if this is still the case?