Yeah the primary scan in Scan it Dental is very messy but very fast, you almost have to guess where the annotation goes, LOL but no worries you can always move them after the detailed scan is complete. D900 and lower scanners can still scan on scan it restoration in 2016 or scan it dental you still have the option to select by enabling scanner features in the control panel. But sort lived in 2017 beta it is removed and my stayed removed i the final launch, we will wait and see. I like scan it dental cause you can scan in any order.
Scanning implant models i find it better to scan the tissue scan first while the tissue is still locked down on the model, then i remove it and scan the marker then the opposing and bite.
Scanning abutment cases, I scan the die first with the hole waxed in and sprayed, then i scan the bite then opposing then model. So many different ways to scan you get to choose what works best for you. Plus the on the fly setting while in the scan window is a cool feature as well. Enable multi die scanning if needed or not, texture as well.
The design layout is very nice once you adapt to it from the 2014. All in all 2016.3 and .4 are solid builds for C&B and implants RPD and dentures may have small hick-ups.