One of the reasons I selected USGS 3 arcsecond DEMS as the format for making BCT/ATF/AATF maps was that it was in a text format that can be manipulated. If you make your alpha value 0, your ATF generated map will use the same north-south as the DEM. You will not be able to get a direct 1 to 1 correlation of the data points, however, because the ATF map generator uses a hard-coded second-latitude-to-meter conversion factor. (28.4 m/s, I think). That means, at least in vertically, the data is in ~78 m intervals, while ATF samples at 100m intervals.
All of that having been said, a program to create or edit ASCII DEMs to add raise or lower terrain would be a great tool. I am not sure it has a broad enough user base potential to justify our building it, but if someone else wants to take a stab, I will give the software the broadest possible dessimination (and, of course, give credit where credit is due).