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I am using clear dock since a long time and always thought that I had to live with that thin hairline that is still visible even though I set the opacity to 0% for everything except the triangle color - but since I have seen too many screenshots now where this problem doesn't exist, I now had to post this question!
I suppose you unchecked "Colorize the Dock Background" ? It's supposed to work for both background fill and border…
If that doesn't work for you, make sure you have the latest APE.
Worst scenario : check Colorize option, but make them transparent ?