Suggestion: Limit Machina growth by player actions.
Element 1: Machina should only spawn in regions where there are active players. If there has been no players acting in a given region cell, no new linking or spawning occurs. Eventually it will die out if no-one players there, and leave the area clear.
This is useful for big fields across regions not being blocked in areas where there are no players.
Element 2: Machina should not spawn new root nodes beyond a maximum level, per regional cell. For example if the maximum root nodes was 10, then once there are 10 spawned root nodes, no new Machina portals will spawn. As long as there's player activity in the cell, it can continue to spread from those root nodes, and splitting a tree in half doesn't mean two "root nodes", since the roots of those trees were infected by links.
This would allow players to pen in and control Machina in regions that don't want growth, but woudl require active maintenance to keep the fences up. Essentially, you'd have 10 corrals in a region that would control the spread, and the occasional saboteur who breaks the fences to let Machina out.
If you cleared out every child of a given root node (connected to it or not) and the node itself, a new node would spawn somewhere in the cell in the next wave.