The primary reason I won has to do with the fact that I took advantage of what I believe are serious flaws in the logic related to special ships that you are rewarded for surveying anomalies like the Nail, Raptor, Ysengard, and Praxis.
Flaw 1: You can create new ship designs that are based on these special ships. This allows you to queue-up production of multiple instances of these ships in all of your shipyards. Since these special ships have lower construction costs and more capabilities than the ships that you could otherwise build, I believe this is an undesired advantage. While it is true that you can no longer queue-up the ship designs that look like the special ships after the first ship is produced, you can get around this by removing the first 2 components that make it a "special" ship. Saving the design without these components will return the construction cost to normal, but you will still have the extra capabilities and you can queue-up production of as many of them as you want at any time.
Flaw 2: For some reason, ship designs that were made based on special ships in previous games appear in the list of ships that are available to build in my current game. The first screen snapshot below shows that, on turn 1, I can build a ship that is based on the Raptor and, as soon as I get some Thulium, I can build a ship that is based on the Ysengard. It looks like the only limitation is the maximum mass that is allowed based on what I have researched. The second screen snapshot below shows that the "Raptor 13.1" ship design has 2 Disruptor Bank weapons and a Carbon Crystal Plating defense component. Clearly, I could not possibly have researched these items by turn 1 which proves that the game is making designs available for production that have components that have not been researched yet. Yes, the "special" ships need to be able to be produced when they have been discovered, but ship designs that are based on them should not. If you fix Flaw 1 by not allowing special ships to be used as a template for designing a new ship, this flaw goes away but, if you decide not to fix flaw 1, you will need to address this flaw.
The way I exploit these flaws is to play a game on the "Beginner" difficulty setting with "Research Rate" set to "Very Fast". As I discover the special ships I do not build them. After I have researched all of the technologies that affect what can go on an ship I then create designs based on each of the special ships that have all of the best components based on each of the maximum mass levels that you can have as you research the technologies that add to the maximum mass levels.
I can then start a game on "Godlike" and these ships will be available to me. This gives me a tremendous advantage over the other civs.