Back when Henry released that report, there were two separate discussion we had relating to freespace. I am not sure which one if either is being referred to, so I will give a brief overview of both.
The first has to do with AGT or average gain test. The discussion was weather running AGT in freespace and over a perfect ground would net the same results. This was more a question of how the software handled the two environments, and as it turns out, it doesn't matter as both environments will yield the same results. One thing to add on this is I know 4nec2 manually removes any form of loss before running AGT, rather than letting the nec2 engine do it on its own. I don't know if this is just being thorough, or if the nec2 engine that 4nec2 uses doesn't always remove said losses on its own, which is necessary for AGT to run properly.
The other discussion had to do with angles of radiation in freespace vs over an earth, and what situations they apply to in reality. It was freespace models that I used to confirm bob85's real world "steering" RF towards the horizon results in modeling. This is something that could not be done if modeled over an earth.
EDIT: I originally wrote the text "two examples" in the above paragraph but only included one. I have a second example, but it may cause more problems than its worth so I removed it.
There is a third discussion that I think may be relevant to what has been posted here that I had with Henry at the time as well. It had to do with using 4nec2 and its ability to give dBm measurements at a given point in space around the antenna. I later found this method to be inaccurate, and since finding this out I have discarded this as a means of measurement.
The DB