Fabscan Pi software saves as .ply cloud mesh. The control interface is via browser, cabled or Wifi. You don't need a screen, keyboard or mouse plugged into it for it to scan - just power and a browser pointing at the right web address (I guess tablet would be fine).
After that, pretty easy to convert to regular STL using Meshmixer or similar. Or OBJ or whatever format. There is already an A500 trapdoor cover on Thingiverse, but no A1200 or A600 HD caddy. Not much in the way of similar trapdoor covers for those models either, so definitely room for improvement.
http://www.thingiverse.com/search/page:2?q=Amiga&sa=
Don't you worry, will be making such things available, for people to test and tweak. "Many hands make light work. "I agree, by the way, scans will need probably need a little work. I figure merging two separate mesh files for both sides of an object. Seems to be an issue with current Amiga 3D models available - there's always a "blind side".
It's a nice scanner, but it can't see straight through solid objects.
