WHM 11.23.0 cPanel 11.23.1-R24909
CENTOS Enterprise 5 i686 on virtuozzo - WHM X v3.1.0
This might be a case of misunderstood expectations I have some cPAddons  which show under both cPAddons Script Feature (default) Manager  and cPAddons Script Feature (disabled) Manager . However, unlike other feature list items, unticking user installable scripts in 3 does not make them unavailable in 2.
 cPanel -> Install cPAddons
 Packages -> Feature Manager -> Default Feature List -> Edit cPAddons Feature list
 Packages -> Feature Manager -> Disabled Feature List -> Edit cPAddons Feature list