(2017) How much of this is still a problem with modern software/font stacks and harfbuzz?
The fact that the article was able to show correct version in regular text is pretty good indicator that if done correctly those are more or less solved problems. I don't disagree that there are probably plenty of times when those mistakes are repeated and solutions not used widely enough (more often for Arabic scripts than other languages), but even for 2017 it feels more like anecdotal examples of what can go wrong…
Luckily it's not a decision without turning back. In most relevant contexts you should know the input language and can select a Font specifically using said variations. Of course this information will not be present in plain text, but if it turns out to become an issue I'd wager, since language codes do exist, that a control code-point for language selection can be added to the specification. There's already so many special cases in Unicode that it shouldn't be a huge issue (apart from backwards-incompatibility that would lead to tofu instead of no rendered glyph).