The style used for The Sanguis Legacy was a breath of fresh air. A change of pace is nice every once in awhile. That said, my personal preference is the chapter format. I don't think you lose anything by going with an alternate route, but my preference does lie with the chapters. I will say that chapters seem easier to plan with, as you can have as many chapters as you want. With the singular format, you run into length issues (is it too short? Too long?).

You can be variant and use whatever strikes you as the way to go at that particular moment. Doing some chapter works, then firing off a one-shot dio just to break up the pace, for example.

Really though, I don't think you can go wrong with either. Yeah, I know that doesn't help choose. As long as something gets released, I can't say I'd find fault with either method.