On the mass driver micro-invasion "exploit," there is another way to rationalize it.
The Devs and others have said that the planetary population # should not be seen as the # of folk on a planet but, instead, the number of folk who are part of the political body and who pay taxes. That is, the # is the # of taxpayers.
So, such a micro invasion using mass drivers could be considered as a "show of force" or a "terror tactic."
That is, many cease to be taxpayers, perhaps due to the demonstrated inability of their government to protect them.
This would explain why the structures are not damaged, but the "population" # greatly reduced.