You can get various emblems, badges, and logo's for just about anything, and some people like to put them on their cars whether they're legit or not (Posers I think they used to be called).
And of course since the MkIV 2JZ was a 3.0 liter twin turbo engine, the emblem/badge you're referring to could well have come from the same place the engine and transmission did and just been worked onto the car. After all, if you went to the trouble of retrofitting that engine and transmission into your MkIII, wouldn't you want to show off a little?
