FDroid's official repository includes fairly strict requirements for apps they allow, meaning you get a level of confidence that those apps meet those requirements. You can add custom repos in the app, but it's not the default flow. To use a recent example, it's like comparing the Arch official repos to AUR.

Not that there isn't value in a tool that can download apps for you from GitHub, but it's not really fair to compare that to F-Droid. You're generally safer on F-Droid's official repo than with random projects off GitHub, and potentially even safer than downloading official releases of apps on F-Droid directly from the releases page.