Well, I think there is more difference than just the type of sensor. I'm not sure the Pertronix is even a real, capacitive-discharge ignition. The literature talks about how it handles dwell, for example, and in a real CD ignition, dwell is just irrelevant. If it's just a points-replacement circuit, dwell still would matter. Also, the Pertronix seems to use four separate magnets for the triggering the spark, which makes accurate timing unlikely. Most magnetic-sensor ignitions use a thing called a reluctor, which avoids that problem.
I put an oscilloscope on a Crane at one point, and was pleased to see that it generates multiple sparks; I doubt that the Pertronix does that--there is a limit to the degree of functionality you can fit into a small package.
As for preferences, the superiority of a CD ignition is so overwhelming, I can't see much reason to use points and a capacitor any more. Some people are concerned about the reliability of the electronics, but the CD is in fact much more reliable than points. Often people say that points are really more reliable, because you can replace them if there is a problem. That argument works until you have to replace them at night, in the rain, in 35-degree weather, and your numb fingers drop a screw into the distributor. And of course, if you are really worried, you can carry a spare ignition module.