I am currently in the same situation and trying to find answers. I have explored and collected everything available over and over while grabbing the red boxes, but there's one entry missing in gathering in all of the exploration zones. In all the screenshots I have seen on twitter where people celebrate collecting all the red boxes I have yet to see a single one who have collected the last gathering item so we're not alone.
As of now I personally think that it's supposed to be the 'Alpha Reactor' item, but a bug causes the progression system to not detect that it's been picked up. I think it's the most likely candidate since the way you get them is through gathering and they are found in all of the zones that have the ??? entry.
Edit (2021-09-18): I just noticed that I now have 100% collected. It was indeed the 'Alpha Rector' that was missing.