Cydia Substrate addons are tweaks you installed via Cydia. You can enable or disable them with a single tap, while still having them installed.
This tool lets you troubleshoot faulty/incompatible tweaks without having to go through the Cydia install/uninstall process.
You can effectively use it to temporarily disable subsets of tweaks until you pinpoint which one is the source of whatever issue you're experiencing.
It is not a substitute for actual Cydia uninstallation, and you should not use it to disable arbitrary tweaks for prolonged periods of time. Doing so is likely going to cause trouble, especially if you disable tweaks that are marked as dependencies of other tweaks.