There are a couple things happening at the same time that we can't do much about. The primary issue is that we don't want malicious content to trick you into modifying security settings. Background: https://en.wikipedia.org/wiki/Clickjacking
Because we're a plug-in, running inside a page, rendered by a browser, it's up to the browser to composite things and determine what's visible, or "on top" of the z-index. It's not clear to us whether or not our security dialogs are visibile. The way that we figure that out is effectively to take a screenshot of the area where our dialog appears. We compare what the browser tells us is on the screen with what we think is there, and if they match, great. If not, we just ignore the clicks. This isn't a perfect solution, particularly if the dialog pops up over something moving, like video or animation.
To address that, we developed the native settings UI (the Flash icon under System Preferences), which it sounds like you found. In that context, we know that your clicks are authoritative, and that the dialogs are visible when you interact with them. Our workaround for when the UI inside of the plugin fails like you described, is to send people to that native UI to grant storage permissions.
Today in 2020, Safari has been getting more and more aggressive about not letting Flash Player access the disk. My guess is that you've granted the right permissions, but Flash can't either read or write the data, or the preference. The application on the website is doing its own check to make sure it can actually store and retrieve data, and then throws the prompt when the check fails. The permissions are granted, but they're not effective per Safari's as-designed behavior.
Your workaround at this point is probably to find another browser for this particular content. Firefox uses the same Flash Player, so it should just work. You'll just need to enable Flash Player in the browser.
https://helpx.adobe.com/flash-player.html
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