It appears as if the script runs on anything that is defined as a beacon and is not something that can be fixed in a separate mod. Disabling the script in its entirety is not a good solution since it will prevent proper use of Py's beacons and I am NOT going to remove Py's beacons in this mod. Attempting to stop just the disabling script would make Py's beacons more effective than bob's beacon 3s, so I don't want to do that, either.
That being said, it appears that you should be able to place the affected entities first and then the beacons without triggering the disable script. You'll have to do it that way if you want to use beacon 2s and 3s.