@Mephisto Style:
There's a difference in your pilot's GP.
The ship stats change with your pilot's GP, but they change at set values. It's like in a role playing game. If I'm 5,000 experience points away from the next level and I get 500 xp, my stats don't change. But those xp still count, and now I need fewer xp to get to the next stat boost.
If you're close enough to the next level, upgrading the color of your current 5-dot mods can make the difference and boost your stats.
If you just barely made your current level, swapping your mods out for lesser-color mods will make you fall back level and that will lower your stats.
If you're in the middle, nothing you do with your mods will count - not boosting them to 6* and not stripping all your mods off your character. If you're too far away from a level break, the stats won't change. But that doesn't mean that green mods or gold mods are still worth exactly the same number of points as purple mods.
Go ahead. Change your mod colors and watch your pilot's GP go up & down. If your ship stats don't change, it's just because you didn't trigger a level change.