FYI, I've also posted this question on https://www.reddit.com/r/qztray/comments/wrfzlo/remember_this_decision_checkbox_disables_yes/.
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Hi, override.crt should be copied to the root of C:\Program Files\QZ Tray\ on Windows, /opt/qz-tray/ on Linux or /Applications/QZ Tray.app/Contents/Resources on Mac as a post-install, manual operation. The manual editing of "qz-tray.properties" should not be needed.
If you'd like to bundle this into the installer, you may do so by recompiling with "authcert.override" flag (e.g. "ant nsis -Dauthcert.override=mycert.crt") per https://qz.io/wiki/compiling#ant-command-line.