If I understand this correctly when we enable one of those factions we are required to cheese with toys from this faction?
That would be an extremely oversimplified understanding
1) There's a difference between "use the ships" and "cheese with the ships". Yes, if you play Golems - Hard and don't
use golems you're going to be at a disadvantage
Though some people turn them on and don't use them because they just wanted more exos in their Fallen Spire game, etc.
2) If you don't want the exos that wipe your fabs and adv-facts, etc, then just play Golems - Medium, it's fairly punishing in its own way but without the attacks that will specifically go for those targets. Or if you don't want to deal with that either, Golems - Easy, and just ratchet up the AI difficulty or pick mean AI Types or whatever you feel
is a proportionate challenge to compensate for the superweapons.
Similar goes for Spirecraft - Hard/Medium/Easy and Botnet - Hard/Medium/Easy. Fallen Spire doesn't have those settings per-se, though the intensity level does control the intensity of the exos generated. But "Fallen Spire - Easy" is basically "do the first two recoveries and just use the refugee's first stage of assistance" and the AI won't do ongoing exos unless you actually build a city.