After playing a while with the new version (haven't played with it since each upgrade tier were individual hull mods), there are a few things that I think might need some tweaks. The biggest one is that almost every NPC ship will have Augmentation Suite installed. The balance for players is the large monthly supply cost increase per tier, but this has no major affect on NPCs. I'm not sure what methods can be used to limit the usage of Augmentation Suite, but in my current game, I'm fighting full fleets of ships with Penultimate Upgrade Packages installed followed by every other mod under the sun. This has the added issue of almost all salvaged ships coming with Augmentation Suite already installed, bypassing the credit cost that would normally come with installing the mod. The second thing is the visual effect of Augmentation Suite. While it's nice to be able to see which ship has it installed at a glance, the effect is too busy. It might be okay if it didn't also affect the shield, but an option to toggle the effect on and off in the Lunalib settings would probably be best, if it's possible.
Otherwise, the mod is working great. Haven't crashed with it so far and the new system of the mod upgrades being a nested option works perfectly. Having a credit cost when installed and upgraded per ship with a supply cost increase is an excellent way of limiting power in the early and mid-game while still providing the fantasy of having a few super ships rather than more and more fleets.