I believe apply_isoxfm is rarely use in conjunction with apply_xfm since the reference volume dictates the final voxel size for standard flirt use (including apply_xfm), that's why i didn't understand what you meant. 

On the other hand apply_isoxfm has a very special usage which is usually only to make the image isotropic, using that image as both the source and target volume. This is quite an idosyncratic use so a separate interface would make more sense.