Spot on Cyber. Zeus hardcounters the whole factory. Sumo can probably do work, but that's not really viable. You can avoid the Zeus's and raid around them, but they're in roughly the same cost range as Pyros so it's really hard.
If I think about it, a lower range, lower RoF Disruptor Skirm might be decent in the Jumpfac. But it has certain problems, which I'm really going to have to go in depth with all the design to talk about. Failing that a Rogue, which synergizes perfectly with the Moderator, but... how do we make it not just another Rogue? A Jumping Rogue? Hrrm. Eh. I'm open to ideas.
So, now for a wall of text on design and roles, if you're interested in understanding the context of the problems here...
This might really be more of a problem with the Zeus. Assaults are anti-static, they don't typically have accurate weapons. The Zeus is an exception but has a low rate of fire, meaning it can be swarmed by smaller raiders. The Pyro is not a smaller raider, so it just gets creamed. Typically this is compensated for by being able to field skirmishers really effectively vs the Zeus, but again the Jumpfac has none. Something worth considering is giving the Zeus a more Halberd-like 'bolt' of lightning. This doesn't really change the fact that the Pyro Factory has huge gaps in it's lineup though.
And that is the really more fundamental problem with the Pyro Fac. There are huge gaping holes in it's lineup, particularly a Riot and a Skirmisher. The Sumo is/was/meant to be a Riot, while the Firewalker and Moderator are both Skirmishers, but the first two are really far out of the weight class of when you need them in 1v1.
Moderator doing damage as it is is not going to work against Zeus though. I agree moderator needs more use in the factory, though I think that's partly the lack of synergy. If given damage it would be able to snipe out raiders and light skirmishers really easily. We could give it a lower rate of fire (and adjust the rate of slow decay as at the moment it's synced with the reload cycle) so it overkills raiders, but that extreme range + slow would make it a nightmare skirm. We could drop the range, make it a proper mass-style skirmisher with a full Disruptor beam. That would work vs Zeus. The perfect accuracy is a problem for this type of unit though, it's going to have riot capacity, hit planes and gunships, etc.
Mass skirms also only stack with more skirms, IE the Recluse ball or the Bouy ball or the Archer ball (a good analogy because they both have movement disables too). This means monoculture. The other thing they stack well with is riots and disables (venom + recluse) but a Disruptor Moderator has the riot and disable built-in.
So the answer might be to add synergy. It should have synergy with the Jack, but the Jack tends to block it's line of fire, and since the Jack is such a dive-in-and-die unit, you usually don't get time to seriously slow the enemy. You kind of need a wall of moderators for this and it's usually better to just make more jacks.
It really should have Synergy with the Firewalker, which is really the Jumpfacs UltraSkirm. Moderator can slow units so they can't catch the Firewalker, and make them spend more time passing through the fireball for extra damage. However, the Firewalker tends to hit the Moderators if the enemy does close range, and you're better off keeping the Firewalker in a defense line. This won't help vs the Zeus either, the Firewalkers DoT is too low.
The Moderator is actually much better when used alongside skirmishers. Rogues and Recluses are incredible with moderators because it makes skirming twice as easy and it makes these inaccurate units hit far more often. The addition of a slow projectile, mid ranged, high alpha skirmisher would synergize really well with the Moderator and completely fix the Zeus issue, but that is, yeah, just adding the Rogue to the Jumpfac... It would be nice if it was different even in a small way. I'm open to ideas. Adding slow to the projectile creates something like the Bouy with less HP (And slow damage only stacks up to 50%, so anti-synergy). It's also worth mentioning that if this unit has less range than the Moderator (It kind of has to), the Moderator can't shoot over it.
The real problem I've been discussing regarding the Pyro fac (I'm saying that on purpose) is that the Pyro is doing all the heavy lifting (Which is why the fac has such issue against a Pyro counter). It's an extreme anti-building raider, a riot, a map control raider, skirms a lot of units and is high weight enough that it also does most of your work during mid game, and operates on a 'retreat-repair' mechanic, like a heavy. It should probably be at least two units, differentiated into a raider and a riot, but there is the question of how this split is made?
The addition of the Puppy was an attempt to give the Pyro fac another raider but since it got the goo mechanic it's been balanced around lategame gooballs rather than early game raiding. Although it's still great in that really narrow situation of raiders that cost more than it and it can 1-shot but when they don't kite it, and is a pretty good mex or wind raider, sadly llt's and solar collectors (!) hardcounter it pretty bad, so it's really hard to use.
It's not terrible in 1v1's. A Jack, Puppy or Pyro start are all viable (A Puppy swarm can snipe a comm and then eat his wreck if you catch him alone). There are lots of ways to play it, but it needs a bit more work to be really reliable and less cheesy.