3D Builder v16.0.2611.0
Collision can be toggled off or on.
Click the "hamburger" icon.
From the menu, click Settings.
Below "Snapping", is "Collision".
Toggle the Collision slider to "Off" so allow objects to be inside one another, so Intersect can be used on them.
Collision does not seem to affect the Object tab "Settle" command.
-ssmeier