..nothing?
C'mon.. This purchase was hardly cheap, I think it warrants that feature at least.
We don't always get the luxury of placing manually printed markers around our scenes. Think about this.. LIDAR scanning feature film sets.. they get BARELY enough time to do this, sometimes late at night (4am, etc) and photo-scanning something could improve this process, as you could shoot all day long as soon as people are out of the shot, then stitch later. But without the ability to manually pick points between photos, your software is relatively useless for this.
Sucks. I'd love to see the ability to manually register points like the GCP setup, but between sets of photos. I'd think just a few manually placed points would make failed scans successful scans.