Thanks for digging into this! The config for the model includes the exact training and initialization settings used to produce the artifact (which is useful because it tells you exactly how it was created), but it also means that you can't necessarily re-run the config if you don't have the same code and data. I guess this is one of the edge cases where Prodigy can't easily be clever and generate a working config from a base model, because it can't know what's in there.
But since you're not training from scratch, you probably just want to source the components from the scispaCy model in your new config, and it's probably easier to just do it by hand.
Sure, you can just replace that block with any other reader – either the default one, or a custom function if you're working with a different format.