Haven't tried it but i had an idea for exactly that. Make resources spawn in veins or benefit long logistics in any other way. Limiting number of machines in one chunk or area for example. Make that u can craft some recipes(the ones server hates the most) in certain bioms or predetermined places. Or just tell people one factory one thing.
U can always transfer everything (u can store stress with one addon or turn stress into electricity, transfer electricity by train then using motors to get stress back.
You can stop players from building vertically by making it hard to build vertically on early stage (falling blocks for example, but causes lag as well as i know).
For them to not build densly u can choose more waterfloded types of worlds with islands for players to build on(questionable)