Whether through an agent or in a structured setting, negotiations are no panacea, probably the opposite, they're a gamble. Some negotiations will always be unfair and deliberately so, in favor of a much stronger party. Just like betting against the house, a weaker party has the odds stacked against them, and is virtually guaranteed to lose, unless they're very lucky. Even fair negotiations in good faith can fail, and there seem no good reasons to assume in her case they were either. It seems very unlikely 'a structured setting' can compensate for all the advantages and leverage studios can bring to bear against individuals and their interests, where a skilled agent could not, with the possible exception of collective bargaining.
If by 'structured setting' you mean something like a union, there's the screen actors guild (how is it different?), which seems to be where these and similar issues should be taken and energies best focused. Studios will of course want the public to believe contract negotiation is s fair process, but will press the laxest, least remunerative terms possible upon actors and actresses. You can try to negotiate for more, but risk ending up with less or nothing for being difficult to deal with. The producer asking her to get half naked might have just be pursuing their interests of their studio diligently as part of their job, in no way extraordinary.
I'm sure she's worked with many male actors who were working as much and as hard as she was who were making much less.
Whether she's richer than some other actors or actresses, let's just consider her among her peers, Hollywood actors and actress, to keep the issue somewhat manageable and fair. To put aside jealousy and envy aside, it's fairly clear many of them are far richer than most of the general public, and much more successful than they will be their entire lives, just by virtue of being there. So we'll just be considering a relatively pampered, mostly undeservingly celebrated, fêted class of vain, unproductive, overpaid, fortunate, self righteous and overly entitled people.
People with more experience should generally get paid more (she's worked since she was quite young), and those (almost a little paradoxically) with more success (isn't that an extra reward?). Distinguishing skill should also be recognized and compensated. Parents shouldn't be penalized for having children (as a broader social concern), though having a family may slow down career advancement nonetheless. These seems truisms for every worker not just actors and actresses.
Appearance is obviously important and has more bearing on thespians than most, e.g. for marketability and suitability for roles. What's to be expected from actors and actresses and how they might be compensated for it in terms of publicity and marketing say, perhaps could be standardized and transparent (it's probably in many contracts already), instead of secretive as it is now. Maybe baring a breast in acting should get a standard rate like losing a thumb does in industry. It would probalby require a group of actresses willing to share and compare their private contracts...
Are Hollywood actresses generally paid less than actors? Probably. Is there generally more intense competition for roles among actresses than actors? Again probably. (I'm not a pollster or statistician, nor studied the subject).
If the latter is true, could be verified empirically, it seems partly just supply and demand. Assuming roughly equal demand for roles and films, if actresses are more plentiful, they should thus come more cheaply. It also suggests also there maybe should not be an expectation of any equality of outcome between actors and actresses. That would be unpleasant news to most would be actresses.
Finally the headline seems deliberately biased; it appears she took great pains to make it clear she's not looking for sympathy, but is just trying to use her high status to help expose what she considers systematic or institutional issues with sexism in her workplace.