In Chinese for instance, you can use a keyboard that combines radicals - parts of a character, or you can use a keyboard that combines phonemes. Those seem likely to change literally how you think in your language. There may be related concerns for Arabic.
That said, one of the complaints in the blog is that two different codepoints render to the same exact letter / phrase / word — this is not a problem unique to Arabic in Unicode, and there are known approaches: I’d expect (I’m not a Unicode expert by any means) that more work on the tech stack for rectification (I’m sure there’s a technical Unicode word for this process of matching codepoints for e.g. search and uniqueness of rendering) would likely be useful for Arabic, and relatively seamlessly flow in many places.