The Precursor Origins tech requires the Ministry of Justice tech. The changes to the tech tree in 1.55 removed the Ministry of Justice tech, so the Precursor Origins tech can't appear, so the tier 3 commander ships don't appear for anybody.
The best way to fix this is to change the Precursor Origins tech to require a tech that does exist in the current tech tree. The tech that seems to be most appropriate is the Colonial Law and Policy tech.
Doing this will repeat a problem that occurred in the base game. The Colonial Law and Policy tech decreases crime, just like the Ministry of Justice tech. In the base game, the Ministry of Justice tech had a preclusion added that didn't allow it to appear for races with the Crimelord ability, namely the Xeloxi. As a result, they could no longer get their tier 3 commander ships. In the current 1.55 game, there already is a preclusion in the Colonial Law and Policy tech, so the Xeloxi can't get it, so they still won't be able to get their tier 3 commander ships with this fix.
In the base game, the "fix" was "unfixed" by removing the preclusion. The Xeloxi could now get their tier 3 commander ships, but they also regained access to the Ministry of Justice, which goes against their beliefs and way of life.
The best solution requires a little work. Before the problem in the base game was "unfixed", I made a mod that "fixed" the problem in a different way. Here is a brief description of what I did, but updated to use the current tech names.
- Change the Precursor Origins tech to require the Colonial Law and Policy tech, and add a preclusion so that Crimelords can't get it. All other races can now get their tier 3 commander ships.
- Create a new tech that is like the Precursor Origins tech except
- It has a different InternalName. I used Crimelords in the name. I left all other names the same so that the correct text would appear in the new tech.
- It requires the Political Capital tech, which is the last one Crimelords can get in 1.55.
- It has a prerequisite so that only Crimelords can get it.
- Change the blueprints of the two Xeloxi tier 3 commander ships to require the new tech in Step 2. This is in StaticShipBlueprintDefs.xml.
I think the above are correct and all the steps I did. I think this fixes everything, but I'm not sure about custom races with the Crimelord Ability. I didn't use this mod for very long before the original "fix" was "unfixed".
The more knowledgeable people at Stardock would need verify everything or maybe come up with a better solution.