Yes, Freight Forwarding overwrites some of the container machines recipes to better fit the progression of that mod. As you've found out, Bob's Inserters messes with the inserter unlock progression, which breaks the Freight Forwarding progression, so in the latest FF update, I've marked Bob's Inserters as incompatible, to stop people playing with them together and wondering why it isn't working. If you'd like to contribute fixes so that they do work together, feel free, but I don't have time to do so (and I generally dislike Bobs mods anyway).