Nathan had a few things he was suspicious of. He had no way of confirming whether the ones the original Nathan or Bianca possessed were the special ones.
After all, those with the special ones would just spread the normal marks. If they only fought Yog-Sothoth, they should only get normal marks. After all, the only ones who could brand them with special marks were Azathoth itself.
However, it would be a different case if Azathoth ended up playing the role. The only thing he could confirm was that the original Nathan had the mark because he was suspecting that the enemy knew everything he was trying to do.
Azathoth could simply come by in one of those timelines and brand him with the special mark. Then it was over.
At the same time, if the original Nathan had the special mark, he might have spread it to the entire continent. At that time, all his actions should be known to Azathoth.
