At the moment the installed packages visible in Package Management are only the ones installed in individual user folders but the packages deployed via spk are not visible (to protect them from accidential deletion as per Case_ID:02077853).
This can result in users installing packages which are already installed in a different folder but in newer versions. Since the package loading sequence starts with looking the user folders it would then potentially use a newer version than the spk deployed one which can cause version conflicts.
To avoid double installations in the first place all installed packages from all .libPaths() should be displayed in package management and a warning should be displayed if someone tries to install a different version of an already installed package into their user folder.
Also admins should have the option to change the default .libPaths load sequence to have the user folders being last and only qualified user could then change that on purpose if they know what they're doing.