"Boxes" in this context almost certainly means "cases of larger size, made to hold merchandise and personal property" (OED). Given the original meaning of "Portmanteau" (see glossary) this interpretation of "boxes" is supported by the next line "So leaves off the portmanteau line and takes unto the trunk line". The railways quickly took over the long distance freight business. (See Theme 005, The Impact of Railways on Horse Powered Transport).