New experimental version!
GC-BTT now initializes the settings menu properly, guaranteed. No more red rows, no more settings not flipping, things should work now even if you've never installed GC-BTT before.
This new version uses a much more intelligent way of making sure that all of the GC-BTT settings variables are set before you are let into the settings window. This way also has redundancy in two stages, so even if the first stage fails it gets caught by the second stage and finishes the GC-BTT setup before the settings window finishes loading.
The first stage was added to the latest BTT alpha, 2.825, and lets you run a named trigger on import. This new trigger sets all the variables to their default settings if they're not already set, and then sets the variable "init_complete" to "complete".
If the first stage was not able to finish for whatever reason - for example, BTT restarting in the middle of the import - the second stage is a pretty foolproof fallback. A JS loop in the settings window itself checks the "init_complete" variable to see if the initialization from the import actually finished. If it didn't, it runs the initialization on-the-fly before it finishes loading the settings menu.
Both of these stages actually trigger the same script - it just gets two chances to finish running. The result is that all the switches in the settings menu should be finally flipped properly when you first install GC-BTT.
We're just a few more versions away from stable now, I'd say 
GoldenChaos-BTT 2.825 (Experimental) Changelog
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[Settings] Improved initialization trigger with "init_complete" variable detection
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[Settings] Renamed initialization trigger so that works with the new BTT feature to run itself on preset import
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[Settings Window] Added "init_complete" check to settings window to prevent against import issues
Known Issues
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[BTT Issue] The menu bar will briefly blink when modifier menus are invoked.
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[BTT Issue] The Play/Pause button may not update properly inside the Now Playing Actions group.