Welcome to the Atlassian developer community @JasonKassies,
To the extent your problem is a function of “how apps work”, this is the right community. There is an aspect of that in your question, but I would advise asking in parallel in the user community. If you haven’t asked there already, you might shift the question slightly to, “On a team, how do you deal with UI provided by apps that you don’t care about?”
From the app perspective, the standard behavior is to appear “everywhere”. To be more precise, apps declare where they want to appear in the Jira UI using specific modules. Some apps, usually driven by feedback from users like you, will take additional steps to hide themselves for certain projects or issues, usually through configuration. But the way to hide per project or issue is not provided by Atlassian; hence, it leaves developers (like this one) to figure it out for themselves.
So, I think the most practical thing you could do is figure out which Marketplace App is providing that “test coverage section” (I’m pretty confident that’s not “native” Jira UI) and ask them to implement a feature to show/hide by project. You might even get lucky and reach a vendor who has already implemented that and can tell you how to perform the necessary configuration (it will vary from app to app).
Hope that helps.