The main story takes place in the 16th century. This means it needs to be before 1521, which is when the Eternals finished their hunt for the Deviants and split up. They mention "one last global sweep", so it's clear this is before that flashback in the movie.
However, the comic shows multiple flashbacks, and one of those takes place in 1520. That would be fine, if the flashback didn't contradict the flashback after. It takes place in 1520, and the flashback after takes place in the 15th century and "a few years earlier" from the main story. This can't be, because then the main story would need to be set later than 1521, which is impossible since the Eternals weren't together at that point.
So, there's either one of these two contradictions going on:
-The comic contradicts the Eternals splitting up in 1521
Or
-The comic contradicts itself with one flashback being dated in 1520. 1502 would make more sense.
There's one other option, which is that the 1520 flashback takes place after all the other flashbacks in the comic, but it doesn't really make sense narratively, since it's clear all the flashbacks build towards the final flashback.
With this in mind, let me know if you guys want timeline placements for the comic.