You can attach skill tree to any pilot you want but if pilot is not directly controlled by you - you don't have access to his skill tree. You can probably make him work like Bryna & KT (teaching new perks by dialog). It's acceptable for one pilot but if you will have to do this for several pilots it becomes boring and irritating.
Other problems:
1. pilots summoned via perk act like mercenaries. They disappear after jump and don't have their progress saved. I can make another perk which will save their perks and exp points but it's a lot of effort.
2. Unlike your storyline pilots they not always end in rescue pod after ship being destroyed. They can simply die.
You can run any function via summon perk. Jump to any sector, open trade station menu, run a dialog, create dust cloud in front of you
- no problem.
Summon perks have number of uses so e.g. you can make perk which summons 6 pilots group once or 1 pilot 6 times.