If it will help you, I've tinkered in the code and it's mostly about the way SE changes beacons:
- beacon overload mechanic(space exploration > scripts > beacon.lua) - essentially to exclude "furnace" entities from the mechanic.
- SE causes all beacons to have their profile set to {1,0} in space exploration > scripts > entity.lua - a loop at end runs through all beacon prototypes.
I've edited those files for my personal save, but obviously it will break on SE update as these are SE file edits.
Might help.