Ey, i haven't said all your stuff is wrong [@Necroes].

I don't see why this is so "not according to fluff" though.
As with GW, they are insane and i try not to think about them. I will admit it. I live in the past in some sort of slightly after 4th edition world where everything was good.

As with the spores, there are squigs and grots long before orks, but i get your point. And i think it was a good choice.

As with the ship, eldar would have been interesting, but we can not really within any sort of sense within the lore understand how to drive an eldar vessel.
The prospect of forcing eldar to work for us is fun. But implausible. However a lot more plausible than driving it ourselves.
But the wraithbone idea was a bit out there. I'm for seeing how one can bend the 40k world and see how far one can go. I added whole new races and stuff when i ran rogue trader once.
But then at the same time there are certain rules. Like bonesingers with wraithbone.

Example of me letting players bend the rules.
When i ran rogue trader, one of the players was the astropath. He wanted to be corrupted.
I saw it as highly implausible, but he came up with a sort of plausible story.
I thought about it, said screw it, and let him be corrupted. So, he got corrupted after the binding, so it could happen that he was corrupted. Also he refused to play if he wasn't allowed to be corrupted.
He could be a bit annoying that way.

Many would say "but astropaths are basically never corrupted, because the emperor has reforged their souls to protect against that." But i say it could happen, so i let it happen.

But then there are factual rules of the setting.
Like you need to be a bonesinger to mold wraithbone. Only navigators can properly navigate the warp. Etc'

I tend to not let any bending of the factual rules. But there are many things one can bend to try and solve problems.
Like a psyker player only having 3 psychic powers. But then the player say "I want to try and emulate this effect with psychic power."
I'd let him try.
It won't be easy, it's implausible he'll succeed. But since it is plausible that the psyker could do it. I'm usually fine with it.

But there's also the question of power level.
"I want to light a candle." Go for it.
"I want to rip the other ship in two." The what now?

All in all, it's a case by case thing.