Well you have gone from a fully protected, can't over drain, can't over charge and in the event of a short it will trip like a fuse, to an unprotected one. The protection circuit (PCM) adds to about ~2+ mm to the bottom of the cell due to the addition of a PCB.
Magnets can be used, but you didn't say the type of mod. In a metal tube mod ya gotta be careful that the magnet doesn't slip possibly causing a short.