Permalink Manager is compatible with all the core Yoast SEO functions. This includes:
- Primary category/terms
The selected terms will be added to the custom permalinks, if the taxonomy tag is present in the Permastructure settings.
- Canonical URL (meta tag)
Why Yoast SEO displays different URL in its metabox?
Yoast SEO uses the native slug to display the URL preview in its metabox. Currently, there is no technical possibility to make it display the custom permalink set with Permalink Manager.
Nevertheless, this issue affects only the Yoast SEO metabox displayed only in admin panel. All URLs (including canonical meta tags and sitemaps generated by Yoast SEO) are correctly filtered by Permalink Manager.