So far I've managed to begin relic boosting 4 toons of course none of which have star fighters. I'm curious as to how the new relic system affects the ship if it makes even a minor impact
No, relics affect ships at every level. Just from flat G13 to R1 you get ~780 GP or so. That's more than you get from 3 6 dot mods. Every relic upgrade boosts the stats.