Is there a way to modify what code is injected via the {squarespace-headers}

I noticed that the {squarespace-headers} injects the meta tags and the scripts into the head portion of the page, but it also injects schema that is incorrect....is there a way to only load selected meta tags and scripts?

Unfortunately, no, except to attempt to individually rewrite all of the scripts, styles, and meta manually by referencing what's rendered client-side. I've heard of a couple people actually pulling that off, but that it likely requires constant vigilance/maintenance to make sure things don't break moving forward.