Yeah, a lot of people really don't seem to grasp that in NGS, Sega is using the traditional style of MMO's where enemies that are significantly higher level than you will take reduced, or in this case no, damage from your attacks, and are still in the mindset of "Oh well it's ONLY one level difference, I'm super well geared, what's the difference!".
It's partly a level of players still not understanding the change in mechanics from PSO2, and another part of people just being stubborn and thinking they're "Helping" by plinking 1-0 damage on an enemy that's five levels higher than they are.
I love the Gigantix concept, it's fun to have a boss that spawns in the world that's not part of an UQ, and actually requires you to have good gear to kill before it despawns, it gives a reason to actually be augmenting all those tier 3 affixes onto your units, awakening your potential on your weapon, hunting for innate potentials, all that fun crap.
But the one thing that is irritating me is, as you said, low levels showing up, and basically ruining it for others. I used Guild Wars 2 as an example before, and again I'll bring it up, as Anet ran into the very same issue when they introduced world bosses that actually required communication, proper builds and end-game gear, to kill. A lot of casual players would join a map, not do the mechanics, and just auto attack the boss thinking it was like any other world boss in the game up to that point, and screw over the other hundred or so players trying to complete it.
Anet's answer was to allow Guilds to create private instances of the map so they could fight the boss themselves, which worked, but it basically turned the world bosses from an organiclly spawning even in the open world, to essentially a one boss raid instance. I don't think Gigantix need that much, they do need to have the scaling adjusted so that people hitting 1-0 damage don't contribute to the bosses scaling, and alternatively don't get rewarded. It doesn't take a full group of 32 to kill a Gigantix, so as long as we can weed out the low levels that aren't contributing, but still adding to the scaling, in some capacity, than that's really all the system needs to be functional without having to rely on creating private instance triggers for them, and effectively just turn them into mini-UQs.