The problem here is that Square Enix is forcing players who are level 50 and have manymanymany things to do, to go back and do leveling content.

I understand the reasoning but many people who are at "endgame" have so much to do as it is, asking them spend 40 minuets+ in a dungeon where all they get is a 1 Animus book kill from the final boss only or a few tomes when .. you need:

27 boss kills, and 13,500 myth of which only consistutes for 10 item levels on just your weapon, i'm sorry to say, that no, most tanks, dps, or healers will want to spend forever killing mobs that take that much more time.

I dont mind the animus books but many people do and this was honestly not a very good approach at all to force people to revisit dead content simply because there is literally no reward to revisit it for reasons besides one boss kill. If each mob had a chance at dropping an Alexandrite, or another Atma, or something worth while you can bet your butt they'd be killing every single mob. Since that isnt the case then, yes you are going go have issues like this.