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You say that that this kind of thing is imaginary, but something like it must be happening when I repeatedly find that a given website/app is in the wrong mode, even though I feel like I've had to switch it before. This is not even a particularly uncommon experience when working with several apps or sites that have the choice, because it's not uncommon for one of those settings to be basically unreadable in some conditions or with font/color choices, etc.
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For reasons (I work for one company, but our work is for both ourselves and sometimes in partnership with others), I often end up with two (or more) instances of certain sites and apps (like two organizational Gitlab instances). To make my life easier, I pick one to be dark and one to be light by default so I can tell at a glance "Ah, this is my corp version, and this other is for some customer". My system also uses automatic dark/light switching.

If I'm setting this up during the day, when I normally work, those external sites would easily end up with the "auto" behavior by this very poor design in the blog, when that is not my actual intent. This would result in me having to set it twice (the second time in the evening) to have my desired behavior which is a nuisance. The explicit option is better here, not whatever this silliness is in the article. [0]

At least I've read this article so sites and apps using this stupid option wouldn't be too big of a surprise to me, I'd hate to have to explain this to other people who haven't read it though. Principle of least surprise is a good thing, not something to deliberately work against like this author wants.

EDIT:

[0] Actually, this demonstrates a crucial flaw in the system's design. If I want to set the current default as the permanent setting, I have to wait until a particular time of day to do so. That's even worse than I'd previously realized. You can only set permanent light in the evening (or by changing your OS/browser settings, changing the site, and then changing OS/browser back). You can only set permanent dark during the day (without that same stupid exercise).

This is a terrible design concept.

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But this means you're "abusing" dark/light mode to signal unrelated information. If some visual customization (theme, font size, etc.) happens to allow you to do something like that, then of course more power to you, but I don't think it has any relevance to the design of the thing itself. It just seems unreasonable to me to expect designers to consider all the ways their designs could do double-duty for any given user (cf. "every change breaks someone's workflow").
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I was just supplying one reason for changing it, other people may just prefer some particular site or application in light mode versus dark (and vice versa) instead of managing multiple instances of the same thing like I am. Suppose you're editing documents and your word processor has dark mode, but you want it to always be in light mode. With the described control in the article you would have to change the behavior in the evening, specifically, to get it to stay in light mode permanently (or change your system settings to be opposite your normal settings, switch it to light, and then switch your system settings back).

There is no way any one with any common sense can think that this two-choice option (one is magic, one does what you would expect; which is which depends on time of day for many users) is better than a three-choice option where each choice does exactly what you'd expect.

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But this change breaks functionality for some people, without correspondingly improving anything for others. So what's the point?

In my experience, software that is designed to work only for the most average user ends up feeling terrible for most everybody, because most people deviate from the average in one way or another, at one time or another.

It feels especially bad when the software makes assumptions about what the user wants, to the point of including a button that doesn't always do the same thing when pressed, and which doesn't even tell the user it doesn't always do the same thing when pressed.

Just look at all the complaints Microsoft gets for the way Windows constantly reverts or ignores user settings.

Or the way it feels to google a very specific set of search terms, only to receive back 20 completely irrelevant listicles that answer a statistically more likely question you didn't ask.

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