Did you read that reference all the way through? It's not at all convincing, IMHO. In nearly all of his experiments you need a gain factor of at least 5-10x before the high frequency range starts to damage the tweeter. He starts with analysing artificial waveforms, and the effect actually lessens as he tries it on more real-world examples. My conclusion: don't play HIA's UFO Detection System too loud? Which no sane person would do, anyway.

That aside, I've always perceived some type of limiter-effect whenever I turn up VLC over 100%. Which is not clipping. I never really considered whether this limiting happened in VLC, the OS or my soundcard. It's a small laptop so no fancy soundcards either.

So, checking VLC's preferences, under Advanced>Audio there's an option called "peak protection", which is on by default. Sounds like something that does a type of limiting?

But I may be wrong, I just checked, (apparently my VLC only seems to go up to 200% by default?), but with a sufficiently loud sample, I could definitely hear clipping, instead of limiting.

But, just like your reference says, at the moment you've applied 5x clipping that's pretty extreme. You might as well have a 1-bit waveform at that point because it'll be either up or down. It won't sound like the original any more, at all. If you play that to your expensive speakers at high power, and think it's a good idea to do that for a while, then I really don't think it's VLC's job to protect you from yourself. The only possible excuse might be someone that has a long playlist of quiet sounds, amped up to 400%, leaves and isn't there to correct it when a forgotten loud track starts up. But that scenario is somewhat far-fetched, somewhat stupid and at 400%+clipping still not certain to damage the tweeters much more than loud sounds might do in general, clipped or not.

And yet, I do not see how a media player can do anything about it.