In my mind, the “SEO-Score” is not lower, if Yoast SEO does not detect your content fields of ACF. While Yoast SEO catches the content out of the correct css selectors or maybe from database, Google & Co. crawl the rendered website content. The difference is, that Google & Co. detect all your Content, although the word count of Yoast SEO displays a value of 0.
So all in all, in my opinion you do not have to raise concern over the live analysis of Yoast SEO, Google & Co. will detect and process your data correctly. I have got a complex website with a lot of custom fields but unfortunately none of these ACF are detected by Yoast SEO. Of course, it would be nice, if the “traffic light” displays a green light and the Yoast SEO Analysis shows me that is all correct but now I have to trust my entered data.
I hope, I could help you a bit.
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