After Permalink Manager is installed it will store the custom permalinks for all new posts and terms. It is possible to edit only selected post types & taxonomies permalinks. In other words, you can exclude specific content types and prevent Permalink Manager from changing their permalinks.
Namely, this could be useful if you would like to eg. use original permalinks for some URLs (eg. pages and posts). Therefore, you can use the plugin to adjust the custom permalinks of WooCommerce permalinks.
To stop Permalink Manager from saving and filtering the custom permalinks please go to plugin's settings. Now scroll down to find "Excluded content types" field. Later, select what post types and taxonomies should be excluded.
How to remove excluded custom permalinks and redirects?
Keep in mind that even if you exclude a content type, any custom permalinks that have been previously saved for that particular CPT or taxonomy will remain in place. This is done on purpose to avoid losing SEO traffic due to URLs that no longer exist.
To remove custom permalinks and redirects from the database, go to "Tools -> Permalink Duplicates" and click "Fix custom permalinks & redirects". As a consequence, the custom permalinks array will no longer contain the excluded post & term items.
"Exclude content types" strict mode
Since the 2.2.20 version, Permalink Manager ignores custom post types and taxonomies that have both the "query var" and "rewrite" properties set to false. This modification was done primarily to prevent the plugin from saving custom permalinks for content items that are not supposed to have their own public URLs.
If you need to employ them for whatever reason, please make sure that the ""Exclude content types" strict mode" option is turned off in the options. As a result, the content types that are excluded by default will appear in the "General settings -> Exclude content types" section.