We're still tracking this issue upstream in Electron. Unfortunately, this is much harder to fix than it would seem, because it is impossible to select the SF system font on macOS directly: you select it by selecting the 'system' font and this is what Tropy does. However, there's an issue in Electron which leads to selection of a poor fallback solution on macOS. We've been tracking this with the Electron team and there has actually been a change proposed back in November. However, this change has not been included in the latest release yet -- but I hope it will find its way into one of the upcoming minor releases.
As a workaround, one thing you could try is to set a custom font in your stylesheet, using a font that includes Arabic characters (it is necessary for the main font to include the suitable glyphs, because otherwise the faulty fallback behavior will kick in).