Years after he had left Marvel, Jack Kirby would answer the questions from the fans at various comic book conventions. He started proposing the thought that Victor only had a small scar along the side of his face. Here is a sketch he drew of it...
Well, check out my
thread about Stan and Jack's appearances in the FF. In issue #10, both Stan and Jack "meet" the Lord of Latveria and Jack is seen trying to cover his eyes in horror at the the sight of Doom unmasked. You can also look at various pictures Kirby drew later on where there appears to be scar tissue around the eyes, or at least what we can see of them through the mask. Stan, for his part, and many writers afterward, always went with the idea that he was badly scarred.
When John Byrne started writng the FF, he had heard from Kirby about the smaller scar idea. So he wrote a tale that reconciled both Kirby and Stan's versions. In "True Lies"... FF #278, Doom's young ward Kristoff has the memories of his guardian implanted in his psyche (the Doombots performed this task since it was believed that Doom was dead after he was blasted into atoms when the Surfer defeated Terrax in FF#260). The memories showed him with a small scar after the failed experiment in college and then when he exiled himself to Tibet, the mask he had forged for himself was still hot when the monks placed it on his face. The second incident resulted in the permanent disfiguration.