I've decided that I'm going to redefine the Pilot Skill Groups for my game. Here's what I intend to use:
Pilot (Personal): Use with jetpacks.
Pilot (Small Craft): Use with fighters, bombers, shuttles, guncutters, etc.
Pilot (Starship): Use with starships.
In Character Creation and Advancement, all cases of Pilot (Flyer) should be replaced with Pilot (Small Craft) and all cases of Pilot (Space Craft) should be replaced with Pilot (Starship). For actions using the Pilot skill, substitue the Skill Group appropriate to the vehicle used.
I have also altered the Shipwise feature of the Void Born Home World a bit:
Shipwise: Birthed in the depths of a voidfaring craft, the void born have a natural affinity for such vehicles. As a result, Navigation (Stellar) (Int), Pilot (Small Craft) (Ag), Pilot (Starship) (Ag), and Trade (Voidfarer) (Ag) are untrained Basic Skills (instead of Advanced Skills) for void born characters.
I added the Trade (Voidfarer) (Ag) to the package after reading the description of the skill and thinking, "Almost every void born should know a bit about this skill."