Yesterday I encountered a spawn beacon which had been placed inside an ammo resupply tower (definitely not on top). Did a full scout out of the tower and could not see the beacon, only the light shining from the top. Had a tank bombard the tower and there was no way to destroy it. This may have been a graphical error but it definitely looked like there was a beacon inside the tower and its sprite was emerging from the top (slightly off center). Should have got a screenshot I guess.
The beam was coming out of the centre on the tower. Tracing the beam down it was either placed under the map somehow or on top and it had disappeared inside.