Every new post/draft has a custom field variable “yst_is_cornerstone” showing

Yes, this is a new Yoast SEO feature. It’s a checkbox, so as long a you don’t select it in the SEO-metabox, the value will be zero/empty. I presume it’s overwritten every time the post is saved, hence it won’t delete or accept a value written directly into the database table.

There doesn’t seem to be a setting in the dashboard, so in order to disable it you’ll have to search the code for a filter or contact Yoast.