Why don't I have all the mod settings? There are only Containerization machine module slots and an Oversized container icon on belts. I use the Freight Forwarding mod and everything related to it.

Freight Forwarding overrides and hides most of the mod settings because it has a very specific idea of the container balance it wants. This mod was split out from FF in order to give more options for people not playing FF.

Is there any way to edit these settings?

Easiest way is to delete these lines from FF: https://github.com/tburrows13/FreightForwarding/blob/master/settings.lua#L32-L38