Is there a repair procedure for outer pipe wall screw holes in the wrong place? Is pre-drilling required for clamp mount screws in the pipe wall?

We definitely don't want screw holes in the outer jacket that allow water to get into the insulation layer. If this happens though, use some high temp silicone, some RTV to cover & close up the holes. Remember to check this when you do the regular inspection of your chimney. Some components wrap around the pipe & provide stability that do not get physically screwed to the outer jacket. The pipe is going to "grow" from thermal expansion when it heats up. As such, the pipe needs to be able to float through things like wall bands, the roof guy kit, etc. Those items don't get screwed to the pipe. In some cases, it is easier to to start by pre-drilling.