They differ only insofar as how radical any change is.
Rationalisation = removing bottlenecks and looking for increased efficiency, usually incrementally. So, reorganising your distribution system so that instead of having three hubs, one in each part of the country, you centralise all distribution, might increase efficiency and accuracy.
BPR = very radical change. one way is to think “If I were to start over again, what would the perfect system be?” BPR might be getting your suppliers to deliver directly to your customers so that you don’t need a warehouse of your own at all.