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Hello @joe16
The Customiser -> General -> Buttons place affects only the buttons that haven’t been customised individually beforehand and buttons that are part of the core WordPress software, such as “post comment”.
Still, some of these options will not apply automatically, since they would be duplicates to options that can be found for each individual button, right inside the builder.
In your specific case – min height – the option will only apply to the “default” header button as well as other buttons such as “post comment”, “add to cart” and so on.
Hope this clears things up!
Thanks.