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Hopefully others with more knowledge may post with better information, but I know that much for sure.
I'm not sure there is any difference or not. I've always just found a ship I liked and upgraded it.
Which is more efficient in case of ship stats
Finding or upgrading
natural s class = upgraded s class
if you have enough nanites you can do the experiment on your own and simply updgrade from c to s and see how the booster slots magicly appear at s-tier
maybe some variety is the base values rng
You don't need a save editor to upgrade your ship class, inventory/tech slots and your multitool class, tech slots.
Just change your difficulty settings to "creative" upgrade for free at any space station and change back to "normal"! Doesn't work in permadeath!
Find Running Mold, set up a base and start farming.
Or go to those who have them open for public and farm till you have enough :)
What he said.
Though, technically, there's no difference between an S-Class you find in the wild and one where you upgraded it (i.e. both have the same potential), the advantage of finding one is that you know EXACTLY what you are going to get before you buy it. When you upgrade, you are stuck with whatever the procgen gives you.
Doesn't matter if all you care about is appearance, as gNg said, but it obviously is a significant difference if you care about supercharge slot placement and/or bonus stats.
I do care about both of those things, so I never upgrade. I can't remember the last time I spent nanites to upgrade a ship.