Yes, scenario B will get you more training. However, I believe your question is about players A & B.
Players A&B receive the same amount of training under both scenarios. It is just that, in scenario two, C will get full training and D gets none. In scenario one, both C and D will get very little training.
Your players will get full training if they get 48 minutes. The drop-off after that is exponential. For example, with 47 mins you'll get 95% training, 46 mins, 85%, etc.
(those numbers are just as an example, I don't know what the actual numbers are)
Run of the Mill Canadian Manager