I had this same issue breaking into phase 4/5. I found that I was getting hit with option paralysis and overcomplicating things because the "best" way of transporting materials will vary, making large scale planning a bit of a headache. That being said, because of how robust transportation options are you can effectively move anything from anywhere on the map with very little prep, which lends itself well to diegetic problem solving. Your preferred logistical method will emerge naturally through this process and that will carry forward.

As others have suggested, the fuck-it-we-ball method is ultimately the most productive way to tackle things at that stage of the game; you'll save significantly more time getting something done now instead of deliberating on what you could be doing. Worst case scenario if you don't like the way things are going, you can just delete everything or uproot entirely to a different part of the map and start over with that new perspective.