The effects of external irradiation on the chemistry and physics in the protostellar envelope around low-mass young stellar objects are poorly understood. The Corona Australis star-forming region contains the R CrA dark cloud, comprising several low-mass protostellar cores irradiated by an intermediate-mass young star. We study the effects on the warm gas and dust in a group of low-mass young stellar objects from the irradiation by the young luminous Herbig Be star R CrA. Herschel/PACS far-infrared datacubes of two low-mass star-forming regions in the R CrA dark cloud are presented. The distribution of CO, OH, H2O, [C II], [O I], and continuum emission is investigated. We have developed a deconvolution algorithm which we use to deconvolve the maps, separating the point-source emission from the extended emission. We also construct rotational diagrams of the molecular species. By deconvolution of the Herschel data, we find large-scale (several thousand AU) dust continuum and spectral line emission not associated with the point sources. Similar rotational temperatures are found for the warm CO ($282\pm4$ K), hot CO ($890\pm84$ K), OH ($79\pm4$ K), and H2O ($197\pm7$ K) emission, respectively, in the point sources and the extended emission. The rotational temperatures are also similar to what is found in other more isolated cores. The extended dust continuum emission is found in two ridges similar in extent and temperature to molecular mm emission, indicative of external heating from the Herbig Be star R CrA. Our results show that a nearby luminous star does not increase the molecular excitation temperatures in the warm gas around a young stellar object (YSO). However, the emission from photodissociation products of H2O, such as OH and O, is enhanced in the warm gas associated with these protostars and their surroundings compared to similar objects not suffering from external irradiation.