Currently, the replytocom variables are enabled by default. The only way to disable it is using a filter
add_filter( 'wpseo_remove_reply_to_com', false );
See gist with more information https://gist.github.com/amboutwe/88f5daa9fbac090e2b6f0c5ff61e3bbb
Users will then need to add the filter into a child theme or download a plugin to help add the code if they are not experienced with editing themes.
In addition, some themes they use the replytocom variable to make it so you can easily respond. For example:
1.Click on the reply and see that the replytocom variable shows

2.The screen then moves you down to where the reply box is

3.Users can then easily fill out a reply.
However, if Yoast 7.x is installed it does not happen
1.Click on reply and see that no replytocom variable shows. Screen then fails to scroll down to where the reply box is.

Other themes like 2017 do not use replytcom and therefore do not have this issue. Even if Yoast 7.x is or is not active replies are still able to be made.
_Yoast not active_

_Yoast active_

Therefore
Re-adding the ability to disable and enable the replytocom variable will provide a better user experience as it makes it easier for users to comment and with more comments it results in more content for Google to crawl and better understand the post/page. This may then affect SEO.
Please inform the customer of conversation # 324288 when this conversation has been closed.
Related thread on our support forums:
https://wordpress.org/support/topic/replytocom-removal-breaks-wp-touch-pro-nested-comments/
Please inform the customer of conversation # 430366 when this conversation has been closed.
This isn't to do with the replytocom variables, it's to do with the ID param of the element in the theme, and whether that's used in the link.
Related: https://wordpress.org/support/topic/readers-cant-answer-comments/
The issue is still actual in Yoast SEO v10.0
Yeah I just ran into this issue using Yoast and WP 5.1, can't seem to understand why this was closed without resolution. The filter trick still works thankfully.
Why is this closed? Still an issue that needs to be resolved (or at least provide documentation for workarounds).
I'm sorry you're having problems. However, this isn't an issue in/with the Yoast SEO plugin, it's an issue with when themes incorrectly use JavaScript to scroll based on the replytocom value, rather than on the individual comment container id value.
If you experience problems with this, I recommend engaging with your theme vendor / developer support.
Most helpful comment
Related: https://wordpress.org/support/topic/readers-cant-answer-comments/
The issue is still actual in Yoast SEO v10.0