you can cut a slot down the middle of the screw driver to compensate for the spoke poking through the back.
True, I suppose
. At that point, you're using a fairly expensive saw, and presumably a bench vise to hold things, to modify a $5 tool... to create an inferior, inconvenient alternative... for a different $5 tool.
I'd have to say the spoke is too long if it's poking through the back and not flush with the nipple.
Yeah, ideally the spoke is very close to flush with the back of the nipple, so that all the threads are engaged.
But in a world of imperfect rims and home-built wheels with slightly wrong spoke lengths, they sometimes stick out a mm or two. That's what rim strips are for :-)