Nothing surprising. Many (misbehaving) programs did check on every start whether they are still registered as startup program an just set the registry key again

Nothing surprising. Many (misbehaving) programs did check on every start whether they are still registered as startup program an just set the registry key again if not. So instead of removing the key when disabling it in Msconfig, Microsoft set a "disabled" key somewhere else so Explorer would ignore them. Sysinternals did not have the luxury of modifying Windows Explorer and so just moved the key to somewhere else, with the disadvantage that the misbehaving program would just restore the registry entry at the original location.