I am enjoying the mod's concept of providing legendary quality machines without the usual grind. However, I suspect the base quality is set to 100%.
To prevent speed modules and beacons from resulting in negative quality percentages, particularly with fluid-based recipes where quality isn't selectable, I propose raising the base quality to approximately 800%.
My testing showed a Cryogenic Plant with Legendary Speed 3 modules and 16 Legendary Beacons (each with 2 Legendary Speed 3 modules) resulted in 180 crafting speed but -700% quality. An 800% base quality might counteract this.
I am also assuming that a quality percentage greater than 100% will simply result in a 100% chance of a quality upgrade.