While I agree it may take longer to see some of the citations that are created with Yext, I don't think the duplicate information from Yext's data push is necessarily bad. It's not like you're duplicating an article - these are local citations which are treated a little differently. Yext is good because it helps create consistency in the local search ecosystem (which is a positive local ranking factor), but i don't think Google dings it for duplicate content. Businesses create hundreds of citations with the same information, yet rank very well. I see that as Google acknowledging the importance of some parts of the data, but ignoring or not positively counting others. Local citations are not "low quality" in the sense they'll help you in local search. Local directories (Yelp, Yellowpages, insiderpages, local newspaper business directories, etc) are valuable in their own way, but only if your intention is to improve local search presence.
To check if the citations are indexed do a site:{citationURL} search. If they're indexed, then Google has found them and is most likely counting them.
The two websites could be working against you, especially if they have similar information on them. Which website do you have tied to the GMB page? Is it the same as all the citations like you mentioned above?