If I may clarify. Pushing the su binary and then the subsequent chmod of said binary to 6755 (or something similar) is what gives ANY application, process or anything else superuser access to your android phone. Consider the Superuser.apk as the guardian. Without installing Superuser.apk AT THE SAME TIME your phone is vulnerable to ANY app using root privileges without your knowledge. That is why it is ABSOLUTELY IMPERATIVE to install Superuser.apk at the same time as the su binary. Do not let any version numbers, etc. get you confused, or even make you think about putting Superuser.apk in /data/app or anywhere else than /system/app. Please do not even speculate about this.
After all, those of you that have done this, every single time an app asks for su, Superuser pops up and asks for permission, right? Think about the alternative. Any app could call for su without your knowledge until you decide to install Superuser.apk from the market. And then, Superuser.apk will be installed to /data/app and a simple factory data reset will remove it until you reinstall it, all the while su will remain in /system/xxx wide open.
I hope this is clear enough and removes all doubt about how important it is to install Superuser.apk AT THE SAME time as the su binary.