Hi there,
Which specific functionality are you referring to? GeneratePress shouldn’t affect the functionalities of Yoast as our code is written in line with WordPress codex standards.
I tested the functionality and it seems to working as expected on my test website: https://share.getcloudapp.com/nOuRRLvy
Are you using a child theme with custom functions?
Or, do you have custom functions in your Elements?
Can you try removing/disabling them temporarily?
Try clearing all caching mechanisms set in your website as well.
Kindly let us know how it goes. 🙂