The points are really only used as a trigger to the CDI box. If the points are gapped at .015" or so, they will properly trigger the box. The actual gap of the points, within reason, has no effect on the duration or strength of the discharge the CDI applies to the Coil. Variances in the gap of the points will affect timing, but that is then separately adjusted by rotating the distributor accordingly. Your dwell checker is only responding to the on/off time of the points. I guess the MSD, like the Bosch has an internal pull-up resistor that the points apply a ground to. Depending on what that resistor is connected to (12V or ??) you might get varying results with your dwell tester. In a conventional Kettering ignition, the dwell/gap setting is important because it affects the 'charging' time of the coil. CDI ignition is different. The points are just a trigger signal to the CDI ('fire now!') when they open. So, to answer your last question, yes ... just set the points gap and then adjust the timing!
