The @id in Schema markup is used as an identifier for the various parts of the Schema @graph – it is not a URL. The Schema @id value can be based on the URL as the @id value must be a unique string.
The WordPress shortlink URLs you provided do not give a 404 – they redirect to their proper pages as they should. See https://developer.projectdmc.org/reference/functions/wp_get_shortlink/ for more information on WordPress shortlinks.
If Google is reporting 404s, then you should determine what those 404 URLs are, as the WordPress shortlinks on your site appear to be working as they expected – redirecting to their post permalinks.
You can tell WPSSO not to use shortlinks under the SSO > Advanced settings page, select a different shortlink provider (Bitly, etc.), or return true for the ‘wpsso_shortlink_disabled’ filter.
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