For how they could tell it was from the first run, it says in the article you referenced:

> For decades, Allen says, nobody knew of a way to distinguish which copies came from that initial run. Then a grader noticed a key difference in a small in-house promotional spot advertising the upcoming Action Comics No. 14. In the first run, those ads included text reading “On sale June 2nd.” Subsequent print runs had updated it to “Now on sale.”