I don't think you & I have much disagreement here as I like the way you write about approximations and edge cases and things involving human judgement calls and "both not either" kinds of testing. The WhyAPCA document you link to also includes language to such effect with sliding scales over regions & such. Me - I'm mostly asking questions not offering answers. That said, to correct the record..
>These examples are using the WCAG2 contrast algorithm which is well known
Only one of the 4 tables shown is the thing you say is the known-to-be-flawed WCAG2 one. Some counterxamples are listed for all 4 formulas, though, 2 of which use the CIE Lightness (which, sure, is probably different, but I believe the CIE L is what APCA is based upon - in spite of so..many..words on their doc pages they often just say "lightness").
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Another point of those 4 tables, perhaps more clear when looking at the python script, is whether "numerical ratio" vs abs(difference) is better. It seems to me that color space designers, like this OKLCH, are going after "perceptual linearity" which suggests abs(diff) is far more appropriate than a "ratio" which has "near zero" troubles (and zero & one are downright seductive numbers for perceptual lightness scales).
I certainly should learn more about it, but various "click through" APCA things I've seen seem to speak in ratio terms like "10 times the contrast" (though admittedly that only assumes some scale for contrast not that it's formulated as a ratio - it's just suggestive). So, I should probably look more into it before actually offering a critique, but it still has the feeling of "cross purposes" - using some color space axis designed for [0,1] linearity differences instead for ratios within that axis. When I tried using the WCAG2 one I was kind of stunned how sensitive everything was to what should have been a kind of "arbitrary adjustment" to handle near-zero.
I might wonder what designers of color spaces actually have to say about this ratio vs. difference issue if you know of any articles. You seem knowledgeable. The spaces seem literally designed for differences to me.