I'll just address 3, because that's most important here.
It is not about significance of the decision, its about the fact we have gross inequality in making that decision, only 2 out of 5 factions are forced to make actual tactical decision impacting their field presence and tech timings directly while remaining 3 just derp around without giving it a second thought.
I'd be equally fine if all potential factions had to make the choice, but they don't, hence it directly impacts balance of tech timing and costs by requirement or lack of it for presence of engineer for specific factions.
Why do you keep coming back to faction equality when we are arguing about a new game. What you seem to be saying is that all factions should be equal in this regard. Why does that make automatons a good change? Why not let all factions build with pios? Do you disagree with my explanation above about why letting pios build stuff is better in terms of gameplay depth?