I'll reply here to both you and baroffoos, it's basically the same question.
> Does this principal apply to X for y?
In a vacuum, yes it's a principal.
In reality, while it's an antipattern it doesn't mean you should be afraid let alone disallowed the ability to exercise good judgement and make a call.
Full window, emersive games are the perfect example of UI elements like buttons that should probably be reskinned - wisely. I say wisely because you can still reskin buttons in a way that affords familiarity you can also reskin them in a way that makes them abhorrent.
A converse example is windows based skinnable hardware interface software like MSI afterburner and the like. That sort of thing is absolute unthought, untested garbage.
For website buttons I think the ship has sailed and the default elements actually look alien.
In fact a lot of CSS frameworks improve net usability from defaults anyway.
Now, is it an antipattern to use them? In essence yes, but considering everything no. Caution, many css frameworks have UX issues and you need to make a judgement in your evaluation about which features to use. I like to see how their autocomplete / dropdown features work it's usually a good litmus test because those things are basically impossible to do right.
And this why we have UX people.
It is the marriage and trade off of usability/hci and designers to create a usability experience that delights.
Though things still tend to lean toward design first approaches. Which aren't incorrect approaches but do tend to lack emphasis on circling back to fix usability later.
I think website internals are widely debatable but do have norms you must consider.
I draw the line at breaking out of the window sandbox and altering browser UI. It assumes all browsers work the same and creates a dependency on the browser for a shared experience.
An inconsequential example: setting browser ui color on mobile version of Chrome. Now your whole website design feels very native and is reasoned about with that native feel. That can them lead to inconsistent design assumptions being made on the desktop. Maybe your color selection clashes badly with the desktop grey.
Like I said, inconsequential, but might illustrate why messing with it might be a bad idea.
The other big reason I throw down at the browser window line is accessibility. Messing with things like button sizing / scrollbar sizing and things wrecks absolute havoc on these users. They also make English centric assumptions about designs that are almost always wrong eventually.