But with breath, while the MCO is practiced with attention only. To my experience when the front chakras are involved into the practice you will have lots of physical reaction and transformation. Still as you do not deepen into the spinal channel the more subtler and inner cleaning takes longer.
SPB and the one from Bihar school will have different effects along the way. Over the very long term I'm not sure if it will go into the deeper nadis within the spinal channel. Most probably you will have different effects with AYP if you combine both over the short and midterm. Over the longterm it is hard to tell as noone I'm aware of finished the job with that combination =)
The front chakras are like the doorway between the "inner" subtle worlds and the physial "outer" world. If you vitalize them by attention and breath you will epxerience a fast merging of inner and outer, but only to the degree of purity and opening of the inner ones. AYP and the Kriya breath taught by Babaji - Lahiri Mahasaya etc. start transforming the inner first while the opening and pouring out to the outer comes a little bit later.
It does not mean the one approach is better or wiser than the other. Just from my own experience, it was more difficult for me to have these fast nondual hapepnings and still being not content deep within. I had too much effects which were distracting from normal life, but in the end its all a question of the balanced application of that practice.
Still if you combine practices, you also may bring different intentions of the opening order together which may conflict earlier or later giving rise to difficulties to continue.
You can try out both systems for a while, later on you'll see which suits you more.
Bihar School of Yoga actually also start with purifying the central channel through the technique they call Ajapa Jap. They use it as a prepatory technique for the kriya yoga with the MCO. In the full kriya yoga there is also kriyas where you work with the central channel like Shambawee mudra.