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A temporary workaround noted here is to go full-screen and then back to normal. Of course that's pretty annoying if it has to be done for every new window. Even automatically in Init Script.. probably feels too jarring.
Another option is to add back a background to the title bar:
Election carried out a fix, and seems it's taking effect in current Atom (1.26.1). The issue still presents on cold start, but if you fullscreen the window and switch back it will recover.
As seen above, the transparency is not aligned and with the transparency on you can click through the actual window, making for unsightly interaction.
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