So I will jump onto the 'I have a theory boat' too. After all, speculation is what we humans do.
I am on the fence...
One way I think it could of happened was this....
She was supposed to be gone. Travis goes for a shower. JA sneaks back into the house and begins taking photos. As a photographer, I know, if you shoot on Auto,you can hold the flash down with your finger and will not flash. (or you can have the camera on manual, no flash and accidently hit the flash button and it will pop the flash up and flash) Also, you can have it on silent shutter and it will not make a clicking noise. That and the shower running, if she was shooting this way, camera glass against shower glass, she could photograph without being noticed. His eyes are closed in all photos until 5:27:18, when in that photo he turns to the shower door and looks directly into the camera (person holding the camera). His eyebrows are arched like "wtf"....
I think she pulls out the gun and begins rambling off things to him, giving him orders, telling him to sit. I believe this because, human nature tells you automatically if someone is holding a knife, although you may be stand-offish and scared, backing down, your mind tells you that you can overpower them to protect yourself...why follow directions of someone simply holding a knife and camera?
She had the gun pointed at him. She tells him to sit, knowing it is a vulnerable position. Snaps a few more, in a frantic state of getting ready to 'kill' him, the flash goes off. The next photos, the flash could have possibly hit her leg, thus not allowing it to extend up and no flash.
I do believe that she shot him first. Why risk being fought off if you come at someone with a knife. I believe he did try to get away or either she dragged him, and then proceeded to stab him. The lack of blood in the cavity? Could it be due to drainage and decomposition? I am no doctor or medical examiner, but is it possible?
Maybe the ceiling shot is when he was trying to defend himself...get away.
*also, shooting on Auto, causes color changes in photos if you are holding down the flash. It depends on where you are standing and can account for some photos having a yellow tint. The circles in some of the photos are what we photogs call 'bokeh'...it is what happens when what is not in focus is in a photo. It creates large circles or blurred shapes depending on distance. The bokeh/circles in photo 5:25 tells me the camera was pressed against the glass of the shower or up really close.