At the end of the day, as in 2018, all of the men and their teams were well aware of the criteria, and made choices accordingly.
In 2018 Ross Miner and his team were well aware in advance of Nationals that he could not just pull two good skates out of his behind and expect to go. In fact, anyone who had been paying attention for more than five seconds knew this. USFS, while not publishing criteria as precisely as on this occasion, had made it clear, publicly and privately, that body of work was the major consideration. This was why only five men were being talked about in the run-up to 2018 Nationals. Miner and his team knew this.
And when USFS published the criteria in August 2020, Malinin and his team - just like every other US skater - were also faced with choices. There were a lot of choices they could make. One of those choices would have been to turn Ilia Senior for the 2021-22 season, push for the Skate America host pick, and push for him to get multiple Senior Bs and Challenger events. Through those events Ilia could have built up a solid Senior body of work, a collection of Senior scores, and a median score to challenge.
But they didn't. Instead, Ilia was kept Junior, with the full acknowledgement of the team of the disadvantage that would leave him at. His team could still have saved this; they could have pursued multiple Senior B/Challenger events, even after the JGP, and allowed Ilia to build a median score that would challenge Jason's. They did not.
And Ilia's median score is lower than Jason's by a margin that cannot be solely explained by the lack of ChSq that Junior men have. Nor even the lack of quads in the SP.
I think what happened was that Ilia made a very unexpected rapid improvement and that the Olympics were never in their original plan.