The implication of the 5e statement is, yes, that an evil god is trying to create something, and gets busy/bored/whatever and doesn’t finish, and somehow an atropal happens. As walen’s fine answer shows,¹ Lost City of Mezro suggests that the specific atropal found in Tomb of Annihilation might be “the Forsaken One,” a “godling born of a profane coupling [of] divine powers,” which doesn’t really seem “incomplete” to me, per se, nor does it really match the sense of “creation” in the implied sense. But then, the suggestion reads to me more like “hey this is a neat tie-in you could do in your game” than it seems like “here’s the canonical origin of that atropal.”
Anyway, prior to 5e, however, there was no implication that this was an abandoned creation. 3e’s Epic Level Handbook states only that they were “stillborn,” so again, not so much “creation” so much as “procreation.” And it need not have been the procreation of an evil god—any god who suffers the misfortune of a late miscarriage is at risk of a significant compounding trauma in the form of an atropal. (The only other mentions of the atropal in 3e that I can find are the 3.5e update pamphlet for Epic Level Handbook, and the atropal scion in Libris Mortis which mentions that the scion’s origin is from a bit of flesh from a destroyed atropal, but says nothing new about the atropal’s origins.)
In 4e, they avoid mentioning stillbirth, saying only that they are “unfinished godlings,” but “godlings” are generally created through reproduction so this to me sounds like a euphemism—there isn’t really any other way to have one that’s incomplete. This still doesn’t quite seem to match the story in Lost City of Mezro where the godling was successfully “born,” in my opinion.
It seems likely to me that the explanation here is just that they’re moving away from the specific, squicky, and potentially triggering, origin of atropals, towards something vague and vaguely compatible. That is, anyone familiar with and interested in using the 3e origin isn’t necessarily told not to by the 5e description (after all, as in 4e, “unfinished” could still be referring to the unsuccessful birth that would have “finished” it), though the mention of an “evil god” kind of throws a wrench in things a bit. But more importantly, anyone unfamiliar with, or uncomfortable with, the 3e origin doesn’t have it thrown in their face now.
Ultimately, though, that’s speculation. The atropal is not a “big,” popular monster with a lot written about it. It’s only really been discussed in any detail—and even then, not much of it—in three publications (3e Epic Level Handbook, 4e Monster Manual, 5e Tomb of Annihilation).² I cannot entirely rule out that it was discussed in some issue of Dragon or Dungeon magazine—this kind of thing would be in their wheelhouse, though again the atropal would be a pretty deep cut—but I’m pretty confident that you won’t find anything else officially discussing the monster.
walen’s answer also includes a transcription of a YouTube fan video that describes the relationship of the Forsaken One’s parents in more detail, and states that instead of being “born,” its mother “tore the unborn child from her womb.” This seems to be a contradiction of what’s said in Lost City of Mezro, and the video does not cite sources, so it isn’t clear whether or not this is original content or is based on some official source. It does notably match the 3e origins of an atropal better than what Lost City of Mezro says, however.
The 3.5e update for Epic Level Handbook only addresses the creature’s stats, in an highly “clinical” way. As mentioned, Libris Mortis mentions the atropal, but only in the context of producing the atropal scion and doesn’t discuss the atropal itself in any significant detail. And Lost Ruins of Mezro includes a bit about the specific atropal in Tomb of Annihilation, but it doesn’t discuss atropals in general much.