A suggestion, while the ethereal bloom has been suggested as a way of keeping an area clear for a small base it has the issue that you've mentioned of being portable so they can basically clear as much as they want with it. There is an alternative option though which can't be moved, give a node in a jar, for example a pure node with one ordo, it requires a wand to use but it means that it's a fairly useless node that just works to turn it's immediate surroundings into magical forest. It doesn't even require the research so you could give it as the result of the thaumonomicon quest instead of the extra thaumonomicon (why is that there?), so yeah as a way of having an item to protect an area without being reusable that's it. For reference the command would be /give <name> Thaumcraft:BlockJarNodeItem 1 0 {nodetype:5,Aspects:[{amount:1,key:"ordo"}]}
As for the actual pack it's been interesting so far, I'm enjoying it so far, I aren't that far admittedly. I've set up base in the tower of a runic dungeon that I disconnected from the ground, it happened to spawn right on top of a guard tower so it's about thirty blocks tall giving me plenty of space. Ores will be a bit tricky due to building over a runic dungeon but at least loot should be plentiful. I'll report more once I've done more then the first couple of quests of different sections.
