Attach the beacons to your favourite teleporter.
There's a tab of Base Items called "Teleport Points" (they're labeled Aleph, Beth, etc.) Put these in the places in your base to which you wish to teleport. The Aleph Beacon will go to the Aleph Point, and so on. The points don't need to be the in same room, so you can now make a base of all rooms with no hallways or doorways. But keep in mind, the beacons need to be in the same room as the teleport device.