Actually I think we still need this as a savegame sanity measure, e.g., to make sure that ruleset changes between saving and loading have not broken things.
So, I think this should be resolved by updating comments, both fit_nationset_to_players() side and the calling side.
fit_nationset_to_players() :
Grepping shows that savegame3.c has a call, though the nationsets were in use by the time savegame3 format was first introduced.