Anyway, this would change crystal from "like metal, but a different color" to a longer-term-planning resource that also serves as an extra way we can balance individually-more-powerful units (due to Lancaster's laws, etc).
Considering this is a long-term plan, I think we're focusing for the moment a bit too much on the overlap with the chokepoint discussion. What does adding a new crystal bring to the table? Fact is, the human command station generates crystal under some of the proposed circumstances. Have too many things cost too much crystal is a recipe for boredom, as to the average player, one who doesn't hit the forum or wiki- it appears to have no cost but time, which is a boring tradeoff. The AIP floor of CPAs is an entirely hidden cost.
If the crystal cost is fairly trivial for fleet ships (keeping in mind the typical build time) than that is entirely fine. If Mk3 and Mk4 more or less keep up with natural income, than I have no complaints with that. Starships costing crystal is a bit more iffy, but all in all positive. Right now, starships are limited by having an extreme disparity of crystal and metal. Spending just metal would make them easier to afford with an entirely automated production queue. Replacing the awkwardness of the heavy bomber/plasma siege inverse m/c costs with a rarer crystal cost would serve a good purpose in my opinion: Making a few choice starships at the beginning of the game is viable without tanking your economy or just hovering at base AIP until you've built everything.
If the crystal cost brought many of the Zenith Trader toys into the realm of plausibility that would be fantastic. Bring down the metal to stress your regular economy but not break it, while using crystal as the reason limit. Your Zenith Trader superchokepoint would be more viable if you were willing to take the external sources long enough to support their creation, rather than having a co-op partner be bankrupt - or unable to repair things - for four out of twelve hours.
On the other hand, I can see leaving crystal entirely out of the spirecraft equation, excepting possibly repair costs. The asteroids themselves are a limiting enough resource.
Forgetting entirely about the mechanics of crystal generation, I've finally grown pretty enthusiastic about this proposal. I'm pretty sure this is worth discussing and coming to some sort of actual implementation.
EDIT: PS: Having crystal be spent on mk3/4 ships and starships both would be acceptable, in hindsight, at the right balance point. At least before the recent starship rebalance, there was a definite intended tradeoff between the starships and fleetships. I'm not sure or not if that's currently true, need to find the time to play a good few sessions.