I think we can disregard the Nako/Yujin theory at very least, there's simply no way. They both ranked very high throughout the entire show and especially Yujin got some god tier edits in the last episode, right as people were doing the final voting.
Chaewon has always been the top suspect simply because Woollim was part of the court case and she shot up into the debut lineup out of nowhere.
Yuri has been considered the 2nd most likely suspect, her debuting would have not been strange at all since she ranked fairly high for most of the show and had some pretty good screentime and edits in the last episodes. The rank of 3 was very unexpected though and that's what caused the suspicions. There's also the whole Idol School thing (4 contestants were from Idol School / Stone Music Ent.) and the last round of voting could have just been the result of those voters converging on Yuri.
The Chaeyeon/Minju version where everyone got moved up 2 ranks I've never even considered but it's actually not THAT crazy, considering that Chaeyeon and Minju got some main character tier edits throughout the entire show, starting from the very first episode. Think about Chaeyeons arc, she made possibly the biggest impact out of anyone in episode 1 and was center in the last episode. She also had massive screentime and the classic MNET underdog story into redemption arc. Minju was similar throughout the show. Considering the screentime and edits its safe to conclude MNET PDs definitely wanted these 2 to debut and removing 2 people while moving everyone up 2 ranks conveniently makes them debut.
That being said I think the most likely truth is that MNET did whatever the fuck they wanted with the rankings and probably shifted around many things, possibly even #1 and #2 (another common claim). All we know is the 2 people that were removed and their original rank, anything else is just a wild guess.
Speculating who was rigged in doesn't actually help the victims in any way but could cause all kinds of harm to the suspects, even though they may not have been rigged in and even if they were, had no idea about it themselves. Ironic thing to say after just theorizing about it myself