I don't know why there is any confusion. It's a single oversize chip. Period.
The fact that the player has no other chips is irrelevant.
It's not the dealer's job to second-guess the player's intention, or to check the player's stack size or contents.
After all, how is this different than a player who has a mountain of 100 chips who puts out a 500 chip when facing the 200 bet? Sure, common sense dictates that the player should use those 100 chips, but common sense goes out the window when you're talking about poker players. So that's a call, just like the last chip scenario is also a call.