That gist looks like a bit of a list of strawman arguments to me. Most of those have never occurred to me, but lets look at one that has
"Stale closures in Hooks are confusing"
Seb gives an example under that section that they call confusing. I don't understand why. The syntax makes it very clear when the values are checked - if its in a closure, its clearly at the time of the click - if its not in the closure, its clearly at the time of rendering, so no, they are obviously not equivalent.
The problem with React hooks is that they behave very differently from all normal JS code. In normal code, most functions that contain closures in them run once and the closures run zero or more times (depending on the consumer of those closures). In React, the render function runs many times, but the inner hook closures run a different (could be smaller, equal or greater) number of times, where that number may depend on the number of times render runs or the number of times other closures run.
You can easily create a mess this way; React realized this, which is why the official documentation recommends not modifying state from within useEffect. But current frameworks (e.g. Remix) already do this, and this already causes problems with batching (see https://twitter.com/oleg008/status/1680290734644002816). Additionally, dependencies between multiple useState and useEffect calls can easily be non-obvious - they may be embedded within custom hooks.
In a mutable / signal based framework that really pays attention to all these details (like MobX) there is a consistent way to how things work based on a relatively simple dependency tracking mental model (MobX based signals can be implemented in about 50 lines of code if we're willing to forego the nice proxy syntax). So not only is state management way easier, its also on average less prone to these kind of issues.
In essence, React state managements makes things harder with the promise of making state easier and more consistent to manage long term, but doesn't really succeed in delivering on that promise. At least not when compared to more newer interations of mutable reactive state management (like MobX) which support all the goodies (automatic dependency tracking, automatic batching, automatic disposal of unobserved state and computed values etc)