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[Goblin Wizard]

You don't need to change any file to add a pilot one of the existing perks. Function pilot:SetPerk("perk_name") is enough and overrides any requirements. You can activate it by e.g. dialog option. This function works with any pilot not only controlled by you or with a perk tree.
Pilots.xml file contains only starting perks for a pilot.
PilotProperties.script keeps definitions for GUI perk tree (with perks costs). Other important parts are two tables inside SaveParks and RestorePerks functions. Their names are self-explainable and are called when pilot leaves/come back under your control.