Well, like the title initially asks, can you really “bulletproof” an Atari AR-II board? From what I have found on the Internet, and older material like Star Tech Journals, the answer really is no. Pretty much all sources that mention “bulletproof” and “AR-II” on the same page are only taking about performing the Sense mods, and nothing else.
A small amount of pages mention replacing parts (caps, regulators, etc.) due to their age, but that is not bulletproofing either – that is just a good idea. But I think I can actually bulletproof it, and maybe other power supplies as well.