I agree that a lot of SF can be bogus, reason why I didn't say "probable", but "possible". Even if the final product is flawed, its manufacturing process tries to be sound (if the author is any good), and in my paltry experience so far, average SF is as much about the how as it is about the what and the other 'W's, giving it an extra dimension compared to average Fantasy (I'm, of course, thinking average books for both SF and Fantasy, with often-used elements in their respective niches).
To be more specific, magic cannot hold a candle to technology (because technology would use LEDs and plasma and gadgets that go "piririp kwitng beep beep") in both plausibility and variety of mechanics. Even if both genres tackle the same ludicrously impossible thing like, say, talking to the dead, I will always see Ubik to be more accurate/possible/creative in its take on necromancy than anything magic has to offer, even if I know the concept is ridiculous. This isn't to say that a lot of Fantasy doesn't try to set up internally consistent mechanics to their supernatural elements (I'm thinking Rothfuss's "empathic links", for example).
What it comes down to, for me, is falsifiability in the methods. We already know lots of supernatural things in fantasy cannot be. Due to technological restraints, there are many things in sci-fi that we suspect cannot be, but we cannot disprove 100%. That in itself grants SF, no matter how improbable the element, an edge in terms of suspension of disbelief at the very least.
With that said: I am a hopeless SF fanboy. Please forgive the literary bigotry. I can't help it. I like Fantasy, but SF is my first love. We tend to idealize first loves and the tendency is hard to shake.
PS: Warhammer 40K is a frustrated hobby of mine. I envy anyone who has it in any form. Necrons were the coolest.