@cviebrock Netlify’s deploys are atomic.
You can read these threads requesting similar ability to “update individual files”:
https://answers.netlify.com/t/api-update-a-single-file/52579
https://answers.netlify.com/t/is-it-possible-to-deploy-only-the-new-changed-files-via-api/87991
If you want the data to be able to be built/deployed without rebuilding/redeploying the other site files, then the way you’ve proposed using a separate site instance would work.
You could also host the data elsewhere and use a proxy.