For those who are curious, I created a private ticket and got a solution for this.
The reason is being, in the latest version of ACF, the field group location options only validate field groups which have been registered for that specific post type. By default are only set for pages and thus not evaluated for custom post types.
This meaning, in the actual template file, we need to ensure that the post type is set in the top of the file.
For example in my template-content-areas.php file i needed the following:
Template Name: Content Areas Template
Template Post Type: post, page, custom_post_type
//rest of page markup here
I’m not sure if this will work for pages as previously stated, the field group location settings “By default are only set for pages”
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