The final version of the story doesn't even include the words "flying saucer" in the title...
...and the ship design itself is closer to Star Trek or 1960s Italian sci-fi like Planet of the Vampires (one of my all-time faves)...
Published in the back of Marvel's Strange Tales #101 (1962), this MadMan-era, never-reprinted, Don Heck-illustrated, Stan Lee-scripted tale was the final version of a Stan Lee plot involving sentient alien spacecraft first used in 1953 (HERE), then re-used in 1958 (HERE), and 1960 (HERE).
NOTE: Atlas had given way to Marvel several months earlier with Amazing Fantasy #15 (first Spider-Man) and Fantastic Four #1 in 1961.
(When Spider-Man received his own title a year later, the FF were cover-featured guest-stars!)
BTW, the cover feature for this issue was the introduction of the Human Torch's short-lived solo strip!
Weird Trivia: All four of the issues these stories originally appeared in had a number "1" in the issue numbering (21, 1, 11, 101)!