Yeah, even disabling a bunch of things and pausing the scene tree, Godot still uses 5% of my CPU (i3-6100T):

  func _ready() -> void:
    set_physics_process(false)
    PhysicsServer2D.set_active(false)
    PhysicsServer3D.set_active(false)
    Engine.max_fps = 1
    RenderingServer.render_loop_enabled = false
    get_tree().paused = true

I wonder what's using that CPU?