What I'm confused about is, extrapolating from the environmental effects from the dust shooting off and possibly completely leveling / rendering uninhabitable parts of the docks, then there's the fact that his weapons systems on display (the mega-laser which can boil off the harder-than-steel scales and dense flesh from an enlarged lung, the 'more missiles in this barrage than Bakuda could dream of putting out' each with exotic effects or powerful payloads, the insane regeneration and durability).
Meaning, there's no real reason he couldn't mount all of that on a weapons platform like his Gundam(s).
Because at this point why are we limiting Apeiron to one mere Endbringer-scale robot? Why couldn't he have multiple?
How is he not an S-class threat, at this point? Politics. Pure and simple. Call Apeiron an S-class threat, and you are disrupting everything about that situation and calling down the thunder. Given the fact that he's operating there on an ongoing basis, and the results of one 'no-holds bar' confrontation with Apeiron is something like 25-30% of the city being essentially destroyed, about the only thing I can see holding that off is Piggot not wanting to lose the other 70% in the crossfire, and Apeiron's duplicates fixing parts (or even all) of the damage while he's unconscious.
Also, while Somer's Rock is still happening--again, how is he not an S-class threat? That's the big question everyone is going to be asking. He's a nuclear deterrent. He's stated, publicly enough, that if you go after the city itself, if you threaten to populace, if you threaten to harm Brockton Bay as a whole, you will become his number one priority.
That completely changes the nature of the game. No one's going anywhere or doing anything while Apeiron is in play. Even your own deterrents like the Empire going after Annihilator capes is not sufficient, not unless they mean to use her. Because Apeiron has demonstrated he is more than capable of just staying out of range and bombarding you with his technology from a mile or more away. He might not even be in the area when he does it, if he can mount those weapons on his drones.
The meeting is going to be more about Apeiron than about Bakuda. That's the knee-jerk reaction here, because while she needs to be dealt with, stat, that's so that she doesn't distract everyone from the real problem.
People see her try her best and fail. Perhaps erroneously, they might attribute that more to the idea that she's not all that great, rather than much like Leet, realize 'failing to do anything meaningful against Apeiron doesn't mean much, lasting longer than a minute matters immensely'.