Multicolumn options in pr imply option -i (tabification). The introduction of tabs with physical rather than logical meaning makes output that is OK for viewing only if you have correct tab stops, and is complicated for further processing. It caters for obsolete equipment--typewriters, on which tabbing was appreciably faster than spacing.
As a wish-list item I propose abolishing implicit tabification. A second choice (that doesn't buck Posix) is to provide an option to suppress implicit tabification. At a bare minimum, document a workaround for the inconvenient tabs, e.g. post-processing with pr -t -e.