The only thing that cannot be changed by mods until now is that cities will accept the generic goods only and nothing else. All the industry chains before the final goods can be changed, even with more steps than “raw”->”goods”.
However, in contrast to all other mods, these cargo mods are very much incompatible to each other because they all change the single list of existing items in TrainFever. You can play with only one at a time. And changing to a different one will force you to start a new game, because the created industries on the map won’t be refreshed. So this sounds a bit annoying to me.
Maybe this will be better solved with the US DLC, which should generally allow switching the environments between European and American – sounds like you might also be able to add more of these to separate the cargo mods.