Exceptions when using this plugin

There are few methods for what you looking for:

1) Turn off Autosort, then add ‘orderby’ => ‘menu_order’ to custom query arguments where the order is required to apply.

2) If need to keep Autosort ON, you can use a filter pto/posts_orderby/ignore to make the sort to apply only for specific post types, see this article for an example https://www.nsp-code.com/ignore-sort-apply-for-certain-query-on-post-types-order/

3) Consider to upgrade to Advanced Post Types Order through which you can use conditionals to specify where the sort will apply.

Thanks