I found two posts that have the same art, but one is in the alpha channel and the other is not. ( post #2160981 and post #2126021 respectively ) Should the one that is not in the alpha channel be flagged as an inferior version or should they just be set as parent/child posts?

It honestly depends if the artwork was originally posted with a background at first and then removed later, especially if someone's trying to cheat by taking a lossy JPEG and removing its background and saving it as a PNG to "improve" it, or if it was created with a transparent background and was saved as a PNG from the get-go.

In the case you've provided, it was an easy answer. The artwork with the white background was taken from Twitter (which converts most PNGs to heavily compressed JPEGs), while the version with the transparent background was the original lossless PNG image. The transparent one was the one to keep.

Ah, OK. Thank you.