Not really.

I typically use the Ninite installer on a clean, freshly installed Windows machine because the installer can be ran again in the future to update those same apps. Chrome/Firefox/etc. will auto-update themselves but for those apps that don't, they will be updated to the latest version if/when you re-run the same installer that you originally downloaded.

If you already have them installed, you do not have to select them, but Ninite will update them to their latest versions if you do. You can also keep the installer it gives you and re-run it later to update the programs.

If you already have them installed, Ninite will detect that and update them (if needed).

It makes it handy to keep the 'installer' that you download, as it will go through and update all of the listed apps later on.

yeah you get a custom installer