Most state laws create a rebuttable presumption that someone breaking into your house is enough to justify a reasonable fear of death or serious injury. It does not say that you can't be second guessed. All it says is that in the absence of other facts, we will presume that the act of breaking into your house alone was enough to justify a fear of death or serious injury (and therefore justify the use of lethal force in self-defense).
However, the presumption is rebuttable - meaning that a prosecutor can offer evidence to show that you were not in immediate, reasonable fear of death or serious injury if there is such evidence.
That's the law in CA.
As a practical matter, it might be hard for a prosecutor to come up with such evidence, and it might be harder to persuade a jury to overcome the presumption, but it can be done.
The way some posters on TFL talk, the evidence might just come from the mouth of the homeowner!
By the way, there is a critical difference between shooting an intruder in your home and shooting someone outside the home just because he stole something of yours or is about to. Let's not conflate the two.