As for playtesting
I dont really see how working out the balance of a shuttle with one less hull point is that different from working out its balance with one more (hull upgrade)?
TL;DR: there are superficial symmetries between Hull Upgrade and Battle Damage, but in fact they're subject to different consequences and different constraints that make Battle Damage at least much more difficult to balance.
Let me demonstrate with a chart:
If What You Gain is...
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| more valuable | equally valuable | less valuable |
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Your List Will...
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| overperform for its cost | be balanced | underperform for its cost |
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I'll assume here that the value of +/- 3 build points is fairly easy to judge, but the value of a hit point varies between ships.
With a Hull Upgrade, then, the designers are giving you the option to give up a quantity with a known value (build points) for a quantity with an unknown value (hit points). If the price of +1 hit point is too high for a given ship, the result is that an upgrade that doesn't work well on that ship, and it just won't get used--not really a balance problem.
With a Battle Damage downgrade, however, you're gaining a fixed quantity (build points) in exchange for an unknown quantity (hit points). Accordingly, errors in the "price" of the downgrade fall to the left on the chart: if the refund is too large for a given ship, there are now builds that are systematically more valuable than their cost.
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To put it another way, if the designers want to minimize the likelihood of an imbalanced upgrade, they can change its price in order to push the result to the right. With a Hull Upgrade, you increase the price; with Battle Damage, you decrease the refund. But there's a lower bound on the amount you earn back from the downgrade--it can't be less than 1.
So if the ship that gets the most value from a Hull Upgrade gets 3 points' worth, then as long as the upgrade costs at least 3 points it doesn't cause a balance issue. But what happens if there's a ship (like the Lambda?) for which that last hit point is worth less than 1 point? Now there's literally no balanced price for Battle Damage.
Additionally, you can look at things from a list perspective instead of the perspective of an individual ship, and now things get really grim. Reducing the price of an Academy Pilot by 1 increases the possible size of a swarm by 1, and likewise -2 means +2 ships and -3 means +3 ships. So as the size of the refund increases, the alpha-strike capability of the swarm grows; a potential -1 discount on the price of the Academy Pilot is a 12.5% increase in that list's initial firepower.
So it turns out we really are--at least for your example--up against that lower bound.
Edited by Vorpal Sword