Honestly I almost never configure the packages on serverside through powershell. But UserConfigs can only be applied to AD-groups. So if you do not set any group, the config will not get applied (I think the cmdlet should fail if you do not apply a group,
but it seems it does not).
The machineconfig does not need a group as it's the default config for the package global wise.
So in order:
1) manifestfile in package
2) deploymentconfig, for whole package
3) userconfig, for specific group