When I talked about throws, that was directed at Jonarobin. Sorry if I wasn't clear enough with that. But doesn't Samus's recovery, the Screw Attack, just go right through the blasts of Elwind? I seem to recall it doing that.
I maybe also should have made it more clear that Thoron is the main spell here, because again, it blasts through missles, essentially locking their use as safe pressure against you. Of course I don't advise to throw out Arcthunder if Samus has a shot charged up. Heck, if you're at a range where Samus can react in time to throw her shot out, then Arcthunder shouldn't be used in the first place, because at that point it'll get blocked or dodged anyway.
I did not intend the tome throw as a means of countering the charge shot. That's not even what I said in the first place. Rather, what I mean by it is that it is a very safe as well as powerful projectile to use, as it cannot be punished with a charge shot. Even if Samus happens to shoot just as you throw, you won't get hit as it clangs. It's a small, quick and powerful projectile, and I'm currently thinking (though this is theorycraft) that it could aid recovery. I should probably add, I don't believe the Levin Sword clangs, because it is weaker.
You can very quickly grab a tome by quickly jumping backwards and pressing the grab button. That's not even close to enough time to punish. Additionally, if you happen to have Thoron charged, they probably will not even consider it, because then Samus is basically inviting you to punish her with it. She doesn't want to take 18% of free damage if she can help it.
You can definitely charge Thoron, I'm convinced of it. Anytime you send her into the air or off the stage, you can charge Thunder. And if it's really necessary, I think you could also jump off the stage and charge there. You can get a stage of Thunder charged and recover safely. Samus probably also won't be over to you quickly enough to punish you in any capacity (heck, if she does try, that may even be beneficial if the punish doesn't happen, because then you'll be closer to her). If you can get to Arcthunder, you can probably get to Thoron too, because Arcthunder is definitely the hardest stage to reach.
Finally, what is a pivot dance supposed to be? I know what pivots are, I know what dashdancing is and I know what perfect pivoting is, but is pivot dancing something else?