Clue (1985) famously had three, true (intentional) alternate endings that were included on the VHS and aired in theaters. It’s not uncommon for alternate endings to appear online after a film is out of theaters (Fatal Attraction, Terminator 2, and others), especially as they're often deleted scenes or scrapped concepts. But Clue used their alternate endings as a marketing tactic while in theaters - you didn’t know which one you’d get when buying a ticket (until they eventually showed them all).
While "director's cuts" occasionally make it to theaters, the recent, on-demand launch of Netflix's Black Mirror: Bandersnatch and Unbreakable Kimmy Schmidt: Kimmy vs. the Reverend has me wondering: did any other films air multiple, true alternate endings in theaters upon release?