The order of ships in the ship selector seems to be partly based on library/extension, not just the SortOrder value on the ships themselves. Because a mod overrides a vanilla type (whether through a hard overwrite or using ShipClassOverride), it gets picked as being from the mod from then on rather than vanilla, which breaks the intended ordering of ships in the lineup. This is visible in all versions of Elemental Shift after I started messing with the Wolfen, and is particularly visible in the (currently unreleased) current version where the Sapphire gets some tweaks and is promptly yeeted out of the first place in the selector.