only allow ST to run on assigned players

Is there anyway to by default  ST not run for new player's and only allow it for players that you allow to see and USE ST?

The most obvious solution would be not to assign any of the skill tree permissions to the default oxide group, and instead create a new oxide group with the permissions attached, and add users into that group whom you want to use the plugin.

Changed Status from Pending to Closed

More or less thinking on joining server a opt in or out option

You would need to use another plugin to handle permissions like that.