If you're changing out the original master for a dual reservoir cylinder for safety reasons, it's hard to argue with that. I'd keep the original on-hand though just in case you decide to sell the car at some point in the future and want to maximize your chances.
The Pertronix.... yes, it can be invisible - but why? Be aware that on a street engine, the notion that you're going to make more power or get more reliability out of an electronic system is wrong on both counts. It won't make any more power, and the thing about an electronic system is that when it goes, it's gone --- there's usually no warning, and there's no bringing it back. Points on the other hand, are dead-nuts simple and reliable.