Myles' Mechanic Guide

I don't believe you can, but the line you quoted was talking about Tank mode, not Prototype, lol

I don't know why anyone would prefer Punch Launcher over Atomic. Sure, it may have more horizontal range, but that doesn't mean anything when you're drilling a map are right in front of the mobs. Also despite Punch having 90% more damage at max over Atomic (with max metal fist), my Atomic /always/ does more damage than Punch. Anywhere from 5k to 10k more.

Probably because of Hammer's ability to ignore defense.

With Heal Bot maxed, there will be a 5 second cooldown duration opposed to 9 seconds. It may not seem like much, but I find it more useful 4th job+ when I won't even be using Drill Rush or Atomic Hammer.

@Locked: If you Party Quest or boss on that character a lot, I'd recommend Siege Mode for amazing 1v1 damage. If you're just training it, I'd recommend Acceleration Bot. Healing Robot should be considered nearly last since it's not too useful while training at this point and it's bugged.
Of course, I'd personally recommend Punch most out of all of those, but if you disdain it, Acceleration Bot -> Satellite -> Siege Mode seems to be the best route.