I noticed another strange behaviour - apparently different hulls with the same default name share build progress as if they were the same hull.

I think I just ran into a version of this bug with the Teros, in r38529.
Looks like it only happens after loading a game where I annexed some neighbors - if I start SiS and immediately start a new game, I only have my own ships available.
But if I load the old save first, then back out to the main ...

That last DOW sounds like a bug - AFAIK there's supposed to be a cooldown preventing that.
(That it doesn't apply when an ally asks for help has been observed before, and makes some sense - but the last one seems straight up wrong.)

Ironically enough this detail is missing from the manual.
(It's also missing what the "Hardpoints" dropdown does - it auto-fills all slots using one of three presets; when you use the Refit option from a planets production menu it also lists all designs you have saved for that hull type.)

But i am not sure what you mean with "toggle on weapons". Did i miss something important ingame? :?
Let me try posting a screenshot...

See how it says "Mods:" below each weapon that's been added to the ship?
Clicking on the abbreviations there toggles the respective mod on or off.

Removing the only counter to a weapon (interception for a missile) is the most drastic, unbalancing thing you can do. There are much more effective ways of improving a weapon if the need is felt for it to be improved.
Maybe instead of making them uninterceptable just give them more health so they ...

Like I said: putting another hard limit on the amount of ships will change this as it gives a secondary value to all ships. In the above particular example: If metal is piling up due to the player having hit the coin limit, the advantage of metal efficiency disappears: If the coin system is working ...

Yeah, it's a feature that's been on my TODO list for years now. One of these days, I may actually find the time to code it up ;)
Wouldn't recommend it: if you have a low entry-level option to simulate battles, that reduces the value of galaxy battles. I have noticed this on myself in Total War ...

Asteroid Stations replace regular Space Stations; they're not supposed to compete with Starbases. It's true that the extra armor is not very useful on a civilian station, but the advantage of an asteroid station is that they're cheaper than regular space stations.

The cost of building a regular ...

The pollution/fallout would be a different metric, but I could see it interacting with the terraforming system. Heavy ecological damage could affect the temperature of the planet ("nuclear winter"), which might push the terraforming meter in one direction or the other.

Sounds good: nuclear ...

What do you mean with "Yorthin"?
Yoral or Orthin?

Lore-wise, I could see "before we started building interstellar ships we experimented with unmanned probes, and collected some data about the surrounding systems in the process."
But that would beg the question why all scouting during the game has to be done with ships...

Probably a bug - I suspect the "AI colonises planet" event gets resolved before the "Harpies attack AI fleet" event.

Do you happen to have a save where it happened, to make it easier to debug?

When humans salvage a battlecruiser, they get the (worthless) 'Battlecruiser' tech. Wouldn't it make more sense to get the tech equivalent, Dreadnoughts (unlocking Battleship)?
Some races have both Battlecruisers and Dreadnoughts (Gremak and Orthin).

But you're right that capturing a tech that ...

The description for the Built-In slots says "Missing INFO"