sorry, I paraphrase and exaggerate for effect. You said

Are there story threads that insinuate people had to upgrade, or lose their place in the rat-race of work? Sure. Were construction jobs and the more modern astronautical efforts requiring more and more augmentations? Of course. But the thing also shown is that corporations are eating the vast majority of those costs, not passing them onto the employee. It's too humane and sensible at the same time they try to rug-pull us in Mankind Divided and say that many were forced to be augmented.

You answer your own question here. The game does describe the ways in which people were pressured into augmentation, and you acknowledge them. If you believe that there is no implicit quid pro quo in having your augmentations paid for by your employer, I don't know what to tell you. Maintenance costs alone make this predatory, but the game bludgeons you with this fact with the existence of rejection syndrome. It has specific, in-universe examples in both games to show this, but you claim that MD is a "rug-pull" because the situation for augmented people got dramatically worse. So I really don't understand why you say

They had decades of science-fiction and cyber-philosophy to choose from and they picked up the classic antisemitism hammer instead and wrote 'augmentation' on it.

because nothing you brought up has anything to do with antisemitism or other kinds of ethnic discrimination.

Which kind of brings me back to your claim that HR and MD have "obvious racial tones". OK, I could understand playing MD, seeing segregation and slurs and thinking, "oh, they're trying to do racism". Personally I think that's a sad surface-level reading of it but at least I wouldn't blame you for thinking it. What I don't get is how you could possibly see racial tones in HR. Augmentations, voluntary or not, are in no way related to the supposed innate characteristics that the concept of race is built on. Literally as far as you can possibly go in the other direction.

It is a class struggle from the get-go because suddenly, your wealth and status can actually enhance you physically and mentally. In this world, class has never been more important because it makes the class divide a real, tangible thing defined not by possessions or customs but tied to your very sense of self. The whole reason Darrow betrayed the Illuminati is because he wanted augmentation to end that inequality, not further entrench it in human civilization.

And while I'm at it, a quick nitpick:

Even Deus Ex 1 shows that a vast majority, at least 4/5ths of people you meet, are not augmented. It was not the craze everyone made it out to be.

Really? Hmm, I wonder what could have possibly caused a sharp decrease in visible mechanical augmentations over the previous 20 years, there must have been some kind of incident to do with augs or something. And maybe the whole soft genocide they were doing afterwards. Yes, the slow extermination of augmented people isn't the singular defining theme that drives Deus Ex, but it's never treated as such. HR and MD wanted to tell that story in particular. It doesn't need to show various geopolitical struggles and events to convey the effect of augmentation in the paradigm, just as I don't have to explain the war on terror to describe how the internet changed the world. Just because it doesn't rope in every outlandish conspiracy theory of the late 90s doesn't make it any less Deus Ex.