ACF for custom post type archive pages: which hook to use?

Is this a sequence mismatch between the hooks?

I would argue so, yes. acf/init gets executed by class ACF’s init method, all in the root file acf.php – this method is hooked to WordPress’ init with a priority of 5 like so

add_action( 'init', array($this, 'init'), 5 );

And you probably add your CPTs with a higher priority, this means acf/init will be executed before the registering of the custom post types.

To solve this, I would hook into init with a even higher priority (smaller than 5) to register the CPTs.