I think there are three main ways to make it work:
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Giving the GM tools to do the job. I remember reading PF2e and thinking, wow, it fills in so many of the gaps I had to improvise on the fly as a DM, and the balancing systems seems to, you know, work. Kevin Crawford's work, especially the ...Without Number series, famously provides so many useful tables guidelines even if you don't use the underlying system itself. Then there are system-neutral resources like the Tome of Adventure Design.
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Providing clear explanations for how and why the system works the way it does. I know it's a love-it-or-hate-it system, but Burning Wheel is great for this. It's a weird system, and whatever you think of Luke Crane, it's useful to have guidance and explanations for why the rules are the way that they are. Plus the Codex adds even more. I found I really like GM resources that explain the thought process behind running the game. IIRC some of Ben Milton's work does the same, and I like to have a commentary for my own projects.
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Giving the players meta-narrative agency. Admittedly, this one is extremely subjective. I have mixed feelings about it. I'm absolutely happy to let my players make some decisions for the game, but I found that my group specifically prefers to inhabit a world rather than shape it, and I'm not crazy about that style of play in practice. It feels more like writing a story than playing it out. TO BE EXTRA CLEAR, this is a matter of personal preference. For those who like it, it works fantastic, and the popularity of that kind of game goes to show how it works for a lot of people.