Worm is a very haxy setting overall. There's a whole category of powers called "all or nothing" powers that are inviolable in some way. For the most part, these hax powers are used for all they're worth, and truly powerful opponents are hurt by far weaker characters wielding high hax. For example, Siberian damages Alexandria with her durability ignoring hax even though Alexandria is much stronger than her overall. Clockblocker's power slices through Echidna despite Echidna being much stronger than Clockblocker.

But the Endbringers scuttle all that. The Endbringers are simply flat out immune to most Worm hax. Matter erasure? Something something space warping something something galaxy level of mass gets replaced and ta da, Eidolon can't matter erase Behemoth away. Siberian? Uh, ignore powers weird physics defying cores blah blah she slips in and falls near the core. Even molecularly slicing nano-thorns for some reason slip through at the denser layers cause "ignores laws of physics." Oh, and blanket immunity from all Master and Stranger and Trump powers period (I mean direct influence, so making minions against an Endbringer is fine, but you can't mind control them or shut off their powers with Mantellum's power suppressing aura)

A consequence of having a lot of diverse and haxy powers in the setting is that it's nearly impossible for a single "top-tier" to beat a massive army of "lower-tiers" single handedly, since it's so much more likely some stray durability-ignoring attack or perfect counter to your abilities shows up and kills you. For plot reasons, Wildbow isn't willing to accept this consequence for the Endbringers. It would be bad for the plot if the first few Endbringers showed up and instantly got gibbed by Siberian's "ignore all durability" or got BFRed into an empty alternate universe by Doormaker Contessa.

But this feels cheap for several reasons. It lessens the impact of super-haxy powers cause it tells me "we're willing to unceremoniously kill off top tier characters with hax but not when it's supposed to be important". And the hax immunity is arbitrarily applied, with Eidolon's tennis court sized matter erasure being lesser to Clockblocker in terms of affecting Endbringers, and Thinker and Master powers all getting screwed over due to Shard restrictions.

Essentially, the "There's a single big threat and literally everyone must team up against this threat" idea doesn't work very well in a haxed out universe, since by nature the fight is going to be a rocket tag. Worm unceremoniously tries to squeeze that sort fight in when doing the Endbringers, and it's even worse with Scion, since the arbitrary limitations placed on Scion's Stilling beams add another level of "the hax are making the plot hard, so let's add plot-mandated restrictions on so that the story MUST end in this way". That's why Scion can conveniently cancel out Gray Boy loops (but Endbringers can't), can't dispel the Siberian (but Endbringers can), can't be predicted by Contessa (but when Contessa becomes a Titan she can predict Endbringers), can't shut off Doormaker portals, but can kill Endbringers with Stilling (Endbringers can't), and can't Still off Sting (Endbringers can't do that either).

Now, I give slight passes to the Simurgh and Tohu. Both of them have powers outside of the hax ignoring that make them threats, so even if Tohu and Simurgh lost their hax ignoring powers, they could still feasibly be huge threats (although I'd still bet on the Parahuman side winning due to sheer diversity of powers).

I will contrast this type of thing with a show like Jojo's Bizarre Adventure. In Jojo, even the very very highest tiers can get screwed over by hax. Diavolo, one of the strongest Stand users with an absolute power that should make him nearly unkillable still has to avoid his identity ever being revealed because he knows how dangerous it is to have La Squadra on his tail. Jotaro, with one of the fastest, most durable, and strongest Stands gets caught off guard by Whitesnake and gets put in a coma. Pucci with Made in Heaven gets killed by some oxygen poisoning. Tooru, even with Wonder of U, goes to great lengths to prevent anyone from knowing his true nature despite his defensive hax. Valentine with D4C Love Train has defensive hax exceeding that of any Endbringer, but even he gets killed when he encounters the absolute offensive hax that is Tusk Act 4. There's not a single moment in Jojo where someone "flexes" off a hax power. Only a much higher hax power can even hope to cancel another one.