Done both and have to say clocking in is the fairest as the boss has a record of your attendance and a visible record of your hours worked.
People used to leave early with no clocking in our place of work and it was all too easy for a boss to accuse everyone of it without proof otherwise.
Every so often a clampdown would occur with the supes chasing around hunting people down 15 minutes before end of shift and catching people leaving early etc.
Some amusing scenes in the carpark etc.......
Some years ago I remember a story concerning a large meat factory taken over by a larger Irish company.
The new director set up a table near the clocking machine and spot-checked anyone foolish enough to clock in for some one else.
All were immediately fired.
Another case I heard of was where video evidence was used to show that the same people who came in late also left early, usually the ones who didn't have to clock in.
New requirements should sort out the short-timers from the on-timers in our workplaces from now on.