The %%page%% Yoast SEO meta template does not work with the Portfolio Index. Most of the tags works. By the way, the meta description setup should be done in the portfolio page. That is the page you've set the Layout - Portfolio template.
The Portfolio page uses the WP Query so I'm not sure if it's an issue with Yoast or X. I'll post this in our issue tracker. But please also forward this to Yoast SEO support. Maybe the %%page%% meta template won't really work inside a page post type even if the page template displays a loop.
For now, regretfully, there is no solution to this but to disallow Google from indexing the Portfolio Index page or use The Grid or Essential Grid to display your portfolio items.
Thank you for understanding.