it doesent scale exactly i cant recall the exact system atm but i believe it works something like this
all ideology perks cost 15 pts
choosing one increases the cost of all the ideology pts in that tree by 10 pts and in all other trees by 5 pts
what this means is that you can focus your tree and collect say all the malevelont traits but that will cause all the benevelent and pragmatic traits to cost 100 pts more then when they started
I feel that, on large maps, it is way too easy to pursue all 3 ideological paths. Imho, once you start down a way by your choices, it should become increasingly difficult to stear your nation toward another path. At present, you can start benevolent, pick the building the produces ideology, make a few neutral choices during colonization, pick neutral, make a few malevolent choices, pick the malevolent building. From then on, you can advance at a nice pace through all idelogical choices. And then, the AI can not cope with you. You get research, influence, morale, diplomacy bonus, inability for the AI to declare war on you until you are ready of have achieved a better diplomatic stance with them - all at the same time. Push a little further down that path, you get free ships + planets&starbases that flip to your side.
Now, there are ways to change that, to make the game a little bit tougher to play, give the AI a chance.
Scaling for large maps is one way to do it.
Another way is to make ideological choices more expensive once you have chosen a path. As soon as you make one choice in pragmatic, the choices in the other 2 trees could become way more expensive. See, imagine real life nations/organizations like the US and ISIS. ISIS beheads people on camera, we shrugg, we expect it. Imagine if we saw a video of US soldiers beheading ISIS prisoners? There would be public outcry in the US and elsewhere. So, the game should try to reflect that, once you are pursuing a choice, it's harder to steer your nation somehwere else.
Maybe the buildings producing ideological traits could be limited to one per colony, meaning that once I build the Preparedness center on my colony, I can no longer build the Missionary Center and Intimidation Center on that same planet. That would probably be closer to what the developpers intended to do in the first place, if I'm not mistaken? It would make it a lot harder to pursue all 3 ideological paths at the same time. It won't prevent you from making "evil" choices some times and a "benevolent" choice at other times, but you won't reap the benefits of all the trees since that is a little bit nonsensical.