40k was meant to be SF from the beggining. The only difference with Warhammer is the background. They weren't made for the same people I think.
And Dwarf Fortress has a Heroic-Fantasy universe. I mean, mixing Fantasy with SF has already spoiled games before, it has to be handled very carefully.
In a game, magic changes the rules that apply to a non-magical world. Tower-cap grows in 3 years? Let's make it grow in one. Let's make rain fall in a less randomly way. Magic just changes the previous rules of the game : in the core, it is said that your adventurer dwarf can't fly. He hasn't got the [FLIER] tag. With magic, you put the txt out of your business and you sort of add it to your dwarf.
That's why magic has to come last I think.
Meanwhile, technology can be used the same way. Just find a non-magical reason : tower-caps will grow faster because you gave it some special fertilizer. And your dwarf will fly because of some anti-grav thing. The problem is a player will always prefer one instead of the other one, and when they'll see the part they like less, it won't do the trick.
If a heroic-fantasy-styled lich was found in 40k, not knowing what all those spaceships are, you'd just be like, What the fuck does it do here?