Wrong application for the beyond reasonable doubt standard?

I have recently noticed what seems to be a wrong application for that standard that is different from known objections related to abusing it and the like. I wonder how those professionals in criminal law may answer it. Here is my point:

The purpose of the standard seems to be clear in that since every person is innocent by default there is a need to be sure of his guilt before incriminating him. That may make sense when person A is being charged with killing person B and there is a need for being sure that he committed that act.But what about situations where it is an established fact that person A killed person B?Would that standard still make sense applied on challenging A's argument that the killing of B was in self defence?

Before whatever actions A claims B took that made him kill B in self defence, we are sure that killing B was a crime. That means we are at the starting point sure that A committed a crime and therefore the burden shift to him to show that it was not a crime. Even if you don't want to require that A makes beyond reasonable doubt argument justifying his killing of B, and I don't know how just that would be, it should still be higher than just making a reasonable doubt on the opposite side's argument that A's claim of self defence killing is false. Otherwise you, as it seems to me, would be empowering easy killing of people. That seems to be especially true in situations where the killer put himself or force a situation on a victim like that case in Florida according to what I currently know.

Let us express that in another way:
Look at this statement:

Did A kill B?

Since we start from the point of being sure of A's innocence (as it is for any person by default) then one needs to remove all reasonable doubts that A's committed the crime in order to move him from the state of certainty  of innocence to that of certainty that he committed the crime.

Now look at this statement:

Was A's killing of B for self defence?

In this case we start from being sure that A committed a crime by killing B. A needs to counteract that certainty with something to undo it. what is not clear to me is how could  reasonable doubt in negating the self defence claim suffice to undo the initial certainty of A's crime in killing B. That may deserve even more attention as much as it was A's choice in making and creating the situation in which ,or even more deserving, because of which the killing occurred.