I'm working on fixing the (many) references to changed prototype names in ATOM and it's associated mods, and I believe I've found a bug.
The item for the magnetising facility was fu_magnet_item and was changed to fu_magnet. So far so good.
The magnet material was fu_materials magnet... and also got changed to fu_magnet. So now items like the EM suspension train require 100 magnetising facilities to make - though you can use the 'cheap' recipe after the first one. So I don't think it actually locks you out of anything, but the balance is questionable.