I understand how to save a set of preferences as a preset, however one of the preferences I am always changing (Use label color in binder) doesn’t seem to exist in the preferences – or am I not seeing it? At the moment the only way to apply that setting seems to be via the menu, so not saveable.
This type of decision, among all of the other tweaks you can make to individual projects, is precisely what the File ▸ Save as Template... feature is for. 
You can read more about them in §5.4, Project Templates, of the user manual PDF.
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