Doesn’t the first Ubisoft Prince of Persia do pretty much exactly what Tim describes in terms of game-overs, ie the game being framed as a story being told by the prince after the fact, with him saying “no, that’s not how it went” whenever the player dies?
RE: games paying tribute to other games, Metal Gear Solid and Splinter Cell had a few back-and-forths, culminating in Sam Fisher’s brief moment of existential crisis in Splinter Cell Blacklist when he learns the other guy “retired” and he’s the only guy still out there sneakin’.