It would also be nice to have the 3 pin manual alignment available between scans on the turn table.

As others have mentioned, you can save the individual scan as a .asc file, and import these into Meshlab, and align them individually in there.

I like the turntable for its automation, but once you begin to realise its defects, you should try using Freescan mode. It takes a little more time, and the results are a lot better, but I can understand why you'd like to see more "step" control on the turntable. If the object has a lot of symmetry in the rotations, the meshing can get confused, and the scanned object has a lot of artefacts. The new "Simplicify" function seems to do the trick, but it loses valuable information on one pass scans, but I haven't tried it on a back to back test with all my previous scan test objects.

Mike