Nah, don't bother drilling new holes. The drives are far more robust than desktop drives (they're desiged to be shaken, moved around, etc. -- they are made for mobile devices after all).
All you need to do to ensure you're safe is to insulate the cradle near the rightmost part with a strip of electrical tape. Some notebook drives have components that might touch the end of the cradle when they're mounted with the only two screws that line up.
I know what you mean by the holes not lining up, some drives have a different screw placement (actually all newer drives have a different placement than older laptop drives) this does not effect the functionality and reliability of these drives in an Amiga 1200 in any way.