Ok thanks @hube2. I had assumed a ticket already existed for this.
I did some digging and turns out it might be a bug in WP. ACF uses wp_get_theme()->get_post_templates(); to get available templates as it probably should but WP_Theme::get_post_templates() fails to request files from the parent theme folder and there are no params or hooks to force it to.
I created a ticket on trac. https://core.trac.wordpress.org/ticket/41717
Going to take a shot at a workaround and I’ll submit here and in a new ticket if it works.
