Right, very typical, I’ve figured out the issue here.
It appears how Shopify labels/names the color schemes in the customiser is index based (starting with 1), and that follows whats in the settings_data.json (above).
So in this case, scheme-3 is the 5th color scheme within this, so its labelled as ‘Scheme 5’ in the customiser but in-fact has an ID of scheme-3.
This is an awful experience IMHO and more the reason to address the below referenced post and allowing us to rename color schemes.
And just an FYI, even though the above has scheme-inverse and scheme-info, it does not display these in the customiser, those are simply referenced as ‘Scheme 2’ and ‘Scheme 3’ respectively.