This transfer process is obviously different to the mechanism for the IFS tanks, which use the standard fuel/resource transfer mechanism, transfer priorities and all. Hence, anything but a reactor from KSPIE is a 'foreign' part. So, I first took the naive step of looking for a fuel pump in the VAB, which I couldn't find.
Therefore, I take your comment to mean that, if I wanted to transfer fuel or waste from the Reprocessor to anything foreign, like an IFS Radioactive Fuel Container, I would need to edit the config file for it to include a fueltransfer partmodule. Having done a reasonable amount of that sort of thing before, I went looking for other instances to see how this is done. Unfortunately, I couldn't find anything that seemed directly related to fuel transfer, nor where to place such a thing.
Please correct me if I have got anything wrong and could I perhaps have another nudge in the right direction?