You may have many custom post types, and WP Related Items plugin can handle all of them if you need.
You may want use WRI Similarity Marker Category for posts and products, but you may do not want to use it for “Music” and “Lyrics” post types (imagine that you have a music and lyrics post types). That is why you can set them separately for each post type.
However I do not really understand this question, because it is just two checkboxes, and you do not need to check them for each products and posts.
But of course, if you use it, then have to be set up it’s values for each post and product, because these values will express the nature of products and posts when the plugin search for similarities. So you do not have to check them for each item (posts and products), but the values should be entered for each item, because each item has it’s own category value.