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I've just started messing around with Genesis because I've heard great things over the years, but I'm having trouble coming up with a good way of implementing changes to function.php and style.css such that... if I ever upgrade a child theme, my changes are not overwritten. Modifying the child theme's functions.php and style.css directly seems to be a bad approach as I'm assuming the developers of the child themes (whether StudioPress or a 3rd party) might occasionally publish updates to those child themes which would then overwrite my customizations. It's similar to tweaking WP core files to customize a site rather than tweaking the theme, just on a smaller scale.
With Thesis, every theme/child theme has a wp-content/themes/<theme-name>/custom/ folder. You make modifications to the theme in this wp-content/themes/<theme-name>/custom/ folder. It contains its own blank style.css, function.php, etc. files. Any changes made to customize the theme are made to those files in the wp-content/themes/<theme-name>/custom/ folder which get applied AFTER the corresponding file from the theme itself is loaded. For example, CSS changes are made to wp-content/themes/<theme-name>/custom/style.css. Then once the theme's own wp-content/themes/<theme-name>/style.css is loaded, it loads the wp-content/themes/<theme-name>/custom/style.css which would contain the overrides needed for the customizations.
The advantage to this is that when the theme/child theme is updated, the files in the wp-content/themes/<theme-name>/custom/ folder are never overwritten, so you do not have to re-implement all of the changes you previously made to the theme/child theme to customize it. They are already there after the upgrade.
Is there any such functionality in Genesis or a plugin from a "reputable" developer that provides equivalent functionality?
Use wpclips.net or custom plugin.
Have another good plugin https://wordpress.org/plugins/genesis-style-trump/ for stylesheet only,
Child themes in WordPress are designed to never send out upgrade notices.
Only Genesis gets upgraded.
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