Is there a way to make a Room which can contain all my Turn Scripts - without preventing them from working outside of that room and it's child rooms?

IE, does EVERYTHING really have to be in a big list under Objects that I can seem to reorder or sort by name, etc?

Unfortunately, organisation isn't always intuitive.

One solution some people use is to put turnscripts/commands into rooms to organise them, and then use a start script which moves them out of the room again. You could give the rooms an attribute "isOrganisationRoom" so you can find them with something like:

foreach (script, ListCombine (AllTurnScripts (), AllCommands())) {
  if (HasObject (script, "parent")) {
    if (GetBoolean (script.parent, "isOrganisationRoom")) {
      script.parent = null
    }
  }
}

This moves commands and turnscripts out of any room with the isOrganisationRoom attribute set to true.