Let me preface all this by saying I run with a naked bed, and this is all info gleaned from several years on the site:
The OEM cover comes with a latch mechanism that hold the tailgate closed. It's not really a lock per se, imagine a gate latch on the inside of the bed. The OEM cover locks down, thus the bed is secure. Without this latch mechanism, the tailgate could be opened with the cover locked.
The Dynolock adds a jamming mechanism inside the tailgate that prevents the handles from working. I believe it can be wired into the door locks to un-jam when the doors are locked, and re-jam when the doors lock. The advantage of this over the latch mechanism is the cover doesn't have to be opened to unlock the tailgate. So it there is snow on the cover you can get the tailgate open without having to clear the cover.
I was wondering if anyone knows where I can purchase a good Tonneau cover like the backflip for a reasonable price or can you recommend a different Tonneau cover that locks and is secure against break ins?