Conversion to MOBI requires rasterization of SVG images. Rasterization of SVG images requires an instance of a browser (Qt WebKit) to be spun up. Presumably something in Qt 5 has changed causing the hidden browser to take focus, despite being hidden and launched from inside an app that has LSUIElement 1 set (which means it tells OS X it does not want any UI drawn for it).
You will notice it with conversion to both MOBI and PDF (both require Qt WebKit).
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