Could you elaborate on your first paragraph? I’m not saying you’re wrong at all - just not quite following your explanation. Start out by defining what you mean by “anti-rattle clips”. Different people use that to mean different things, and I want to understand what you mean by having “too many” of them.I don’t know about the scan tool, but another thing that will cause the brake pedal to go down too far is some one putting too many anti rattle clips on the brake pads & seizing the brakes up which overheats the fluid , then you go from having fair brakes to almost no brakes!
I didn’t do this someone I asked to do my brakes because I really didn’t feel like doing it really helped me “ out” so that’s why I do my own work!!