I'm not sure why one would want to set the number to negative? and is it possible that its somehow an intended feature? like how sometimes -1 is set to denote infinity?
One could set it to negative so that ships start the battle with their maximum mitigation, and have enemy fire or certain enemy abilities decrease mitigation.
For example, all ships enter a battle with 100% mitigation, and are unable to be harmed. An ability on some ships that applies only to energy weapons decreases enemy shield mitigation, so these ships and their energy weapons are required for any fight to go anywhere. Not sure about about it being an intended feature, the setting he describes is used for how much shield generation decreases each [second?]. Were it maximum mitigation, it rising to infinite would make sense for a -1 being infinite value. However, were that to hold for this setting shield mitigation should drop by an infinite amount, meaning you only ever have the minimum shield mitigation.
To whoever asked if Mitigation percentages over 100% meant the ship healed, yes, yes it does - at least for Trinity. Accidentally ran into that with a mod I was making where I was toying around to see how mitigation worked. Ended up having a ship that couldn't die. Did this at a Pirate base, and wiped the whole thing no damage taken [Or so it appeared].