Interesting comments. I like how some are so sure of themselves, and others are so eager to consume whatever is fed to them.
I use a Cannon, always have and probably always will, so my comments are not directly applicable to all other units. I also use electrics now - got tired of cranking up balls.
First, how does your auto-stop work (you know this means Electric Downrigger don't you)? Mine stops when the mild positive ion field (electric current) is cut as the SS clears the water. If I replace the SS with braid then I must hold the up switch all of the way to retrieve the ball. If your system uses a similar design, then your up switch on your "Electric" downrigger will no longer be automatic. Is this a problem, well, only you can say.
Second, Blow Back is not what comes out of your back side, but it may be what comes out of his mouth. The correct answer is that Blow Back is the angle the ball "blows back" or drifts behind the boat as you troll. The amount is dependent on the speed you troll, the weight of the ball, the design of the ball, fresh verses salt water, and the type and diameter of your cable. There are tables that give you a guide and you can find most of this from the manufacture.
If you fish shallow, perhaps under 50', and slow, maybe under 2 mph, and use a 10+ # ball (sorry, I don't keep my charts on me so this is a swag), then your depth change due to blow back is minimal. But, if you are fishing at 150', trolling at 4 mph, with SS or a heavy diameter braid, you may actually be fishing only 130 or less feet deep when your counter measures 150'.
It is very true that SS cables have a whine or growl as you troll. Braids do not seem to have this. I can't tell you it does not make any difference, but I do believe you can compensate for it. The same is true for any transient electrical charge.
Let's start with electrical charge. If you use SS with an uncovered lead ball, you may leave a negative ion trail. Most so-called experts claim that this is a problem. Of course you can go with a "Black Box", or you can make sure your boat is properly grounded (negative battery post grounded to all exposed metal contacting the water) and use a coated ball (rubber or epoxy works well), or you can go to a braid. Alternately, you can just let your lure out more before you hook it to the ball. No ion trail last more then about 30 to 50 feet behind the ball, so if you let out 75' of line before you hook up then all is well. The choice is yours.
Now, noise. Letting your lure out more will allow super finicky fish to relax after the noise is past. Of course, braid has almost no noise, at least that we can hear, so this is an option. Here is the problem.
I only have one rigger, but I have had friends set up pretty much like I am. One of us always seems to be rigged with braid, and the other seems to always be using SS. We seem to change back and forth. Some days the fish seem to prefer the noise and charge the SS brings, while other days they seem to prefer the low noise and low charge of the braid. In an ideal world I would love to be able to change out quickly - fat chance.
For the record, my current position, subject to change at least twice a year, is that SS offers me more options. Nevertheless, both Braid and SS work, and both work well. The choice is up to you, and no matter which one you take, it will be the right one, at least part of the time.
Too much water, so many fish, too little time.