And it also may have been a cold-blooded murder of opportunity by Dad, so yes, we could speculate all day about exactly what happened and I am not discounting anything.
I still feel though, if he claims he shot an 'unidentified intruder' he should have had better control over who had keys to the house before doing so regardless of the time of night.
If he knew it was the ex-boyfriend and claims he had motive, that is something else. He still should have controlled the keys, of course, or changed the locks.
If a key gets lost to my house or I have any doubts at all about a copy being made that I do not know about, I change the locks for precisely this reason.