Both methods are equally valid.

With target based registration you only use targets acquired in the field to stitch together the data you have collected. However, you can add automatic cloud constraints on top off these to get a more accurate fit if required, or correct any errors in target acquisition during data-collection.

With Cloud to cloud registration you have to provide Cyclone with a hint as to the orientation of the scan positions and then the software will automatically place the scans for you based on some pre-defined parameters.

Both options give you diagnostics to trace the accuracy of your registration and allow you to tweak and amend as necessary to get the results you require.