Oh, this is not a bug, I can see what is happening. If you are replacing a submodel, all other submodels in the game with the same value will be replaced.
So if you replace "Coupe" with "Awesome", you will end up with all coupe's being awesome (e.g "Lamborghini Gallardo Awesome").
Since you are replacing a blank (??) with something, everything else with no sub models will be replaced, since the internal value for ?? changes from blank to GTI.
That's why the ID field is located next to the value field. For cases such as this, or unrenamable cars such as the Edonis or Ascari, you change the ID.
For example, load up TDUPE, go to the Golf and change the submodel ID to:
78882366 and press save car. This will change load a different value that is not in the game (Toyota Celica in this case). Change Celica to GTI and enjoy.