I can enter any of the factories, place any item in the factory control chest, leave the factory and have inserters taking the items out on the outside of the factory when i leave it... Go back inside and the items are still in the chest, able to repeat for free infinite items.

Yeah, noticed that accidentally too today. Fun stuff.

I'd have used combinator displays instead of containers for the overlays, but the combinator info overlay is disabled by default in the settings, so containers it is. Unfortunately I'm not aware of any reliable way to make the inserters stop taking things out of the display containers, so it's up to you to avoid using this exploit.

No big deal really. :)
Maybe it is possible to add a check of display & chest contents when entering a factory? To destroy the missing items in the chests if they were pulled from display.

That method couldn't really distinguish between pulling something from display and adding it to the chests. I'd need to compare the display contents with what I put in them last time.