I think the question is if he should put the keeper wood against the fence, or on the outside of the blade. I do not do a lot of resawing, but I normally put the widest part (be it the the part I am going to use or the stock I am cutting that board from) against the fence as it is more stable that way. So, for me, it depends on the overall width of the stock vs the width of the piece I am going to use.
In this case, if I understand correctly, he is basically splitting the board, so I would put the keeper portion against the fence, providing I have the fence set where I am not getting any drift. If there is any drift tendency, I would have it go into the waste wood.
Again, I do this rarely, so those that use a bandsaw frequently may want to correct what I have said.