reproject
does what its name suggests: it reprojects pixel data from a single image to a new image with a different scale and/or orientation. If you look at the example they show in the QuickStart, this converts the MSX infrared (E band, ~21 microns) image which is in galactic co-ordinates with a pixel scale of ~24"/pixel to the same scale and orientation as a 2MASS infrared (K band, ~2.2 microns) image in RA, Dec co-ordinates with ~5"/pixel pixel scale.
montage
, and its wrapper, also does this reprojection but can also perform mosaicing where you combine multiple images, normally with some (~20%), overlap into a single larger image.
I didn't see anything in the reproject
documentation that states that it can handle multiple images i.e. the mosaicing part.