Overall the factory abilities don't necessarily need to be equal value, just one more variable in balancing the wholeness of the factory.
Factory sidearms in general seem tricky for the reason Anarchid mentioned, targeting vs. rally point. Maybe the engine has a way of dealing with this?
Tank Welder sidearm seems fair-ish because everything in that factory is slow to build, so it's risky to plop offensively. Would be scary to fight a self-defending factory in your backline which produces Ogres. The extra health was intended to support this without being a raider deterrent or a free turret plop with 4k health.
For hovers I think either a (disarming?) anti-air or anti-sub sidearm might be appropriate, because Flail is relatively slow to field, anti-sub synergizes with being able to build on water surface, and offensively plopping these kinds of weapons is less prone to cheese.
I imagined the shield being Convict-strength, something to give a little nudge to Aegis in base. You could pack it full of Caretakers to prevent hugging, but then your production chain explodes. Maybe shields should get limited Racketeer sidearm instead. Still, plopping in range of enemy factory lets you shut down all their bp early game.
Jump factory might need a different idea, maybe Newton sidearm or Lobster capability to boost allies onto adjacent cliffs.
Cloak Factory could itself be invisible, but as soon as you add a Caretaker it seems easy to find. If it cloaked the unit in production this would be marginally valuable counter-intelligence. Imagine plopping a Cloakbot factory and pumping out Scythes and Phantoms completely invisibly.
Another change I would like to make is for Cloak factory to be the only thing that can produce Iris, because it is one of the strongest units in the factory but everybody else has access to it. Nobody can morph into Minotaur, Felon, Grizzly, Domi, Raven, Lance, etc. Corona and Iris don't even look similar to each other.
