If I remove an entry from the run line of the registry that starts a certain program. I am not removing the program.
Can you see the difference in that, your example is removing program entries, my example is removing an entry to have a program run.
Same thing when MSCONFIG is used to disable a program from starting, it's not touching the program or any part of it.
Exact same thing as removing a scheduled task. it's not part of the program.
If I delete my scheduled task to run disk defragmenter I am not removing any part of the program o making any changes to the program.