The programs that hijack your settings commonly do so to get you to a site where additional malicious crud is dumped on your machine. Without knowing exactly what a program does, it would be very difficult to be certain that all unwanted effects have been removed. It's fairly common for the "analyses" of these things to include "possible other unknown functions" in the description.

It's difficult enough with many of these just do get them removed. Attempting to "modify them to your own purpose" is akin to having a sick person spit on your baby in hopes of making baby immune - to something - when you don't really know what disease is involved.

John