Can two GoPro Hero3 cameras be made to capture the same frame from the same spot?
GoPro Hero's are frequently used in the kind of capacity you describe.  It is possible you got some defective units (as certainly the time lapse stuff for the silver is a bad unit), however much of the problems appear to be user error rather than camera problems.

In your overlay shots, the frame appears to be consistent, they just aren't pointed in the same direction.  Keep in mind that a very small amount of variation in positioning will result in a drastically shifted image.  If you are just setting the camera on a table, picking it up and putting another one down in the same place, I would expect results like you are getting.

To really do what you are trying, you need to get a mount for the purpose that will hold the GoPro's in proper alignment.  With many cameras, this type of rig is a custom job, but for the GoPro, things like this are done so often that you can actually buy pre-made rigs for them for things like 3D shooting, 360 degree shots (or even video), time lapse tracking rigs and other forms of multi-shot rigs.

If you get one of these mounts and are still having problems, contact GoPro about the problem because they should be consistent.