If it was actual non trivial content I could see the problem. Crystal Tower bosses and even Copied Factory can be completed with several dead players and even current ones can be as well so it isn't like they are asking you to complete something that is ridiculously difficult or that requires an insane amount of effort. Anyone can complete these one time to see the story then never do them again.

I really doubt there's some conspiracy here, something probably happens in 5.3 that would make less sense if you didn't do the crystal tower quest line as some of it relates to an existing character so they just put that in there for continuity sake.