A homepage built using a page builder that uses meta data would not affect SEO any differently to one you built 100% manually (wrote all the HTML yourself in the post HTML editor).
Wordpress uses PHP to create the HTML browsers download and render, which means that everything search engines see is the final output (HTML). If you use a page builder that uses meta, you may not see it in Wordpress' post editor, but the end-result is the same as if the content were visible in the post editor. Also, Yoast may not be able to analyse your page, but as long as the theme/page builder outputs internal-seo-friendly code, then it is fine.
In short, it definitely doesn't make any difference whatsoever.
I am about to release a new theme and developed, what I believe to be, a fantastic drag and drop page builder for it, that has all its data completely stored/manipulated using meta. It makes for a very enjoyable and high quality user experience. I used shortcodes on my first theme, and even though they work fine, they make for a very, very bad user experience, and I am never going back to them
P.S: As someone who has a lot of experience in SEO, I can safely say that to rank in search engines the most important thing is still high-quality content and a good portfolio of backlinks from relevant, good external sites.