Hi Ryan,
The spreadsheet in our example also uses the Copioli Method [I basically took Paul's example and added the source generator tabs

], so it follows that you get the same generated results.
It's not clear what you're observation is. Are you saying the generated profile doesn't match your expectations? If so, exactly what is wrong with the generate profile screenshots that you attached? Those plots seem reasonable at first glance.
...Or are you saying the physical motion of the mechanism isn't matching your expectations? If so the specified cruise-velocity/acceleration may need to be tweaked, or gains need to be adjusted to better honor the generated target profile.