First you should note that Cydia Substrate requires you to have “root” access on your device. Cydia Substrate may be incompatible with your device, but will attempt to detect this. There is also an irritation with many HTC devices; Substrate has a new workaround in it as of June 1st (0.9.4008) that should allow it to work on these systems.
Cydia Substrate is simply a platform for customizing software. Due to limitations of the Google Play Store it must be installed separately, but its primary purpose is to support other products: users should not expect Cydia Substrate itself to do anything interesting. Instead, it should be thought of as enabling your device to support other things you may install.
Some products that use Substrate are able to modify other programs, whether it came with your phone or was installed later, or whether it was developed by Google or a third-party developer. Though, these kinds of changes carry an inherent risk: changes to the underlying software being modified may break the modifications (“extensions”) you installed.
It’s very important you note that Cydia Substrate for Android is new. its developers have spent alot of time testing it on different devices with many versions of Android, there is always the possibility that there’s something unique to your setup that causes an incompatibility. If possible, I recommend that you backup your device handy; I’d also recommend being setup with a recovery mode image that allows you to easily delete this app.