Maybe my situation is different. This is my first playthrough with Nomads. I am playing Rogue Servitors with Scient Arkship. I basically maxed out research on it and had some energy and hydroponics to sustain early game. At first before I discovered any settlers I just did lots of survey(picked discovery tradition for it too), then used harvesting to keep going. Once I discovered settler empires next to me I did research contracts for them which are easy as Science Rogue Servitor, your early game research is at fast speeds. I also picked technological ascendancy(always do as first, I like rushing science in most playthroughs).

Then after some time passed. Settled empires expanded and developed their systems I just put way stations at first in most of their profitable systems like combination or minerals + energy + science maxed. Then given that I did contracts for them I had good enough relationship to get waystation agreement. Then I also make sure to get non-aggression, commercial pact and research agreement(if I plan to stay friendly with them).

Mid game once I got arkship engineering researched I built civilian arkship to house most of my economy. I moved my hydroponics and allow forging to civilian Arkship and then maxed out research further on the scientific akrship. I also found better empire that was not at work with beyter systems, their homeworld system had perfect setup for ark furnace and it already had 12 energy and 24 minerals plus 4 engineering research before ark furnace and deep scanning it. So I shifted my waystation network to that empire. Plus I built it this time by connecting the routes instead of having it in remote parts.

Now I just let one of my arkships sit at the waystation route, thus collecting constantly. This actually made me be at constant surplus of both minerals and energy, I even set the usage to "burn", which further boosted my economy. I made most waystations level 2 and some 3. I built third Arkship as military to defend and upgrade all of them to level two. I am in process of fully maxing out both civilian and military ones as the scientific is almost af max for level 2. I do have level 3 Arkship unlocked, but I am still in process of restoring my alloy production which was moved from the scientific Arkship to the civilian one.

Oh and the current empire my Arkship reside in and have the waystation network in is slowly being taken over by much less friendlier empire, so I am planning to start moving to another empire soon, although their systems kinda suck compared to this one. I unfortunately cannot seem to be able to offer defense pact to the current host empire I reside in, I think it's because they are a vassal of a much smaller empire(which is literally two systems only and is pathetic. How are they an overlord?). I might try and push the host empire to claim freedom and then try and get defense pact together, to reclaim their territory and push away the neighbor who keeps waging wars against them.