OK. I see the problem. Unless WP were to update the term_relationships table so it could distinguish object_ids as belonging to a user or a post, the potential for conflict is unavoidable.
My main goal is to run taxonomy queries for a user. It would work about as well for me to run meta queries for a user except that ACF stores the taxonomy terms in a serialized array in the user_meta table. I don’t know of a reliable way to run a meta query that looks for a value in a serialized array. If ACF stored taxonomy term ids each as a separate user_meta fields, then I could effectively run a user meta query. I realize that would be a big shift for ACF and I don’t expect you to take it on.
I’ll likely solve this by creating my own user-taxonomy field. Since I know in my particular instance I won’t have term taxonomies shared between posts and users, I’ll probably store the taxonomy terms as such but I may explore storing them as separate meta fields instead. I very much appreciate that ACF is built with enough flexibility to make it straightforward for me to create my own field for this.
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