In all of these cases, both versions of the song are combined into the same entity, which generally looks better overall because in the long run, a lot of the remix versions are relatively short lived, even if it is admittedly a bit misleading. Of course the opposite happens as well, to this day, Skrillex's remix which was relevant for about a week is still how ARIA credit HUMBLE.. There's no rhyme or reason to it, ARIA are just very messy and at times lazy with their data.
The Ed and Beyonce edition of "Perfect" hit the charts on 11th of Dec, 2017, and that was also the week that the song went to #1 nationally, while on the last week of the year (25th Dec., 2017) the Andrea Bocelli duet was the better seller, after which the three versions of the song (solo Ed, or two duets) all charted together.
So in summation the Ed & Bey duet was the top seller for two weeks.
I feel like a lot of the time it's automatic. Feature credits are missing all of the time because of the way Spotify deals with its meta-data, and ARIA just grab it without looking unless they take enough notice of the track (eg "Bad Guy" being capitalised because it debuted at #1 but nothing else on the album). You also get ugly credits like 'SHAED, ZAYN' for the same reason which occasionally get fixed when the songs climb higher on the chart, but this recent example has just been left like it.
But I think you rarely see these remix versions credited because it requires going out of their way to do so.