"Base timing" has to do with the orientation of the internal parts of the P-Mag.  If you wanted to use it operationally, you would have to mount the unit at a precise angle in the mag mounting hole.  Others on the LML have reported some degree of difficulty doing this. So, the folks at E-Mag devised a quick setup method where you can mount the unit in any orientation and then "program" that position as TDC (with the flywheel so positioned).

This option only became recently available with firmware version 16 so earlier versions would not have the potential problem and if you do have the later version you should contact E-Mag for the fix.