This actually happens with the other beacons as well, just to a lesser degree. It depends on whether the beacon's diminishing returns take into account all beacons, or just beacons of the same type. Unfortunately, there doesn't seem to be a way to account for all normal beacons and only exclude the invisible beacons added by Stable Foundations.
The diminishing returns for most beacons are balanced around different beacons potentially affecting the same machines, so I think Stable Foundations may not be fully compatible with most beacon mods - at least those which use diminishing returns or have "normal" beacons. I can fix this for isolation beacons and other "solo" beacons by making them only take into account themselves, but that solution doesn't work for beacons which are meant to be usable alongside different beacons.