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But you don’t [refer to them by hue]

People do it fairly often. Specially when precision is needed. Vermilion red, ultramarine blue, so goes on.

that’s why languages lacking these words run into issues as described in the article.

The issue is not lacking a word, but mismatching usage - in this case, between Japanese as used by the speakers versus the legislation. It wouldn't happen if the speakers kept using 青/ao for emerald-coloured stuff - they'd look at the emerald-coloured go light, say "it's ao!", legislation agrees, all is well.

And it is certainly not directly the result of a lack of words for those six arbitrarily specific tones, as this example shows:

The soil in the picture is called "terra roxa" in Portuguese. It means "purple soil" (red soil would be "terra vermelha"). It's the exact same underlying issue as in Japanese - you call it by one name, and yet the underlying colour is another.

And, while there are potential three reasons why it might be called this way (old Spanish explorers, Portuguese internal change, Italian colonists), all of them involve some mapping mismatch:

And yet in no relevant moment the language lacked a distinction between red and purple. On the contrary - it has three words for that range. ("Púrpura" is nowadays mostly a fancy synonymous for "roxo", but based on Galician usage odds are that all three were distinct at some point; for reference modern Hungarian does it too).

But isn’t there a good reason it was distorted that way?

That's mostly appeal to ignorance - "we don't know, so it's caused by this".

That distorted colour wheel is likely the result of the access to pigments and traditional usage back then, and lack of access to knowledge on how our eyes process light.

Also note two things:

• before synthetic dyes there was little practical use for a specific word for blue.
• the biggest distinction, the one that you see across all languages out there, is missing from those six colours. It's "dark" vs. "light".

You won’t run into the issue of differently coloured traffic lights in english countries

A "country" speaks no language. That is not just nitpicking - the issue is a mismatch between the language as used by the population vs. the legislation.

And yes, this issue could happen if English remapped the colour used to refer to green, through some semantic shift.