5.25" disks include a synchronization index hole read by the drive and 3.25" disks align using a hub mechanism. These wouldn't be too difficult to align factory-duplicated floppies in a custom jig that includes a laser or similar small, focused heating element.

The risk of this style of approach is that it must be compatible with every single drive manufactured combined with every floppy controller because it must produce exactly the same OS-level error pathology with intentional physical damage. (Another approach is inducing low level MFM errors without physically modifying the media but it requires special hardware.)

Also, as with physical hasps (dongles), copy protection magic codes, install floppy disk writable decrementing counters, damaged sector key disks, and pretty much every other technique, these checks always exist somewhere as binary instructions in the executable and can be located with a debugger and/or hex editor through binary search and/or call stack tracing heuristics in a relatively short time.