I agree that the logical way to handle that is with an organic constraint, not a hard limit. My suggestions in rank order:

1. Implement a maintenance cost and track it for each CSL ship-type based on average ship age. Make the decision to retire ships based on the ship-type's profitability (income earned by the ship-type minus cost to build minus accrued maintenance cost). Once a shipping line reaches a certain age (10 years? 20 years?) start check annually whether each ship-type profitability is above a certain level act accordingly. This will naturally cycle out older ships and reduce overcapacity of specific ship-types (because idle ships cost maintenance and earn nothing, so they'll eventually be retired), with very limited computational load.

2. Allow the player to determine (on the wealth tab) how much to tax colonist ship tonnage and cargo ship tonnage (individually). This would give players the flexibility to encourage or discourage growth by giving the CSLs more or less income and hence driving growth (and/or contraction if idea 1 were implemented). This would only require adding two numeric fields on the wealth tab, so hopefully minimal programming work.

3. Can CSLs please be allowed to move minerals based on mineral reserve targets? Moving minerals around manually is one of my least favorite tasks, as it's pure drudge work on a repeating basis that adds little to nothing to enjoyment of the game.

4. Very strongly support the previously mentioned idea of getting more granular colony population controls. Some ideas:
4a. Ability to set TRANSPORTATION target, as in "transport 1m people here" (vs "bring people here until it hits 1M"), because then you don't risk massively overpopulating smaller colonies if your civilian lift capacity is large
4b. Ability to set a min/max target transportation RATE per year, as in "transport 1M people here per year" or "Take no more than 5m people from Earth per year"

I get that armed civilians would give you that East India Company vibe but for any other type of setting, it would not fit at all. Airlines do not operate fighter jets and Maersk does not own any battleships. I'm strongly against giving civilians the ability to build armed escorts or to put weapons on commercial designs or civilian ships.

Beyond this, it also would not work very well for gameplay. If the civilian ship armaments are not very good, then they're basically useless and just a waste of civilian ships. If the armaments are actually useful, then there's no real need to defend civilians from Raiders if they can do it themselves, so a key new area of gameplay is basically trivialized. Probably best not to do that...

I get that armed civilians would give you that East India Company vibe but for any other type of setting, it would not fit at all. Airlines do not operate fighter jets and Maersk does not own any battleships. I'm strongly against giving civilians the ability to build armed escorts or to put weapons on commercial designs or civilian ships.

How are systems generated in Known Stars games? The wiki says "The game works through all the stars in order of increasing distance. There is a 20% chance of selecting the nearest star, then if that isn't selected, 20% chance of second nearest star, etc." I think this is from the old VB version, but I haven't seen any posts about changes to this. I ran some tests in a fresh game generating systems from Sol and they seemed to confirm the 20% number. However, in my games I've also seen systems with really distant neighbors, like HIP 31293 in the screenshot. Its neighbors have distances in real space of 54.1, 63.1, and 70 light-years, and as far as I can tell there are hundreds of closer systems that haven't been picked yet. So it seems very unlikely to me that this was generated purely by iterating through the closest systems.

Is there any way to transfer a population to an NPC?