The only settings that get preserved are the ones in the GC-BTT settings menu! The preset is designed to be used unmodified, since all the settings switches in the settings menu do the rearranging. However, since you made deeper changes - like those dividers and significantly rearranging the layout - you'll need to recreate those changes when you upgrade. My suggestion is to basically ignore the settings menu if you're planning on manually editing things in BTT.
It's possible that there will be a way to upgrade similarly modified versions in the future, but there's no time frame for that currently - @Andreas_Hegenberg did talk about being able to override existing widgets on import once which would be fantastic.