Michael Mann films like “Heat”, “Ali”, “The Last of the Mohicans” and “Manhunter” were altered by the director on video (though I believe the latter two do have their theatrical versions on modern formats).
“The Devil’s Advocate” had to digitally alter an artwork for legal reasons. “Mulholland Drive” had the nudity blurred on DVD by David Lynch himself (no idea if this happened on the Criterion Blu-ray, or if Lynch’s concerns about nude pictures circulating online still apply).
On less critically-acclaimed films, “Battlefield Earth” and “Highlander: Endgame” were modified on DVD (the latter known for blurring out a giant JVC logo, not for legal reasons but because the filmmakers found it distracting).
“Stand by Me” reportedly had an alteration during its theatrical run, with the text on the monitor at the end refined.
Do the “Raiders” alterations still exist on the Blu-ray? I recall Spielberg a few years ago changing his stance on special editions (comparing his newfound agreement with purists to how outraged he would be if someone did wire removal on George Pal’s “The War of the Worlds”).