Hi David:
Could be both. Practice yields purification, and purification yields practice.
However, there can more going on here than metabolism alone, or the lack of it. The breath reflex can also happen when there is no lack of oxygen -- a quick and shallow in-breath or out-breath, or a series of both, which is automatic bastrika. In that case, it is an impulse arising from inner silence (samadhi) stimulating it, not necessarily a metabolic adjustment. Bastrika can happen like that, riding on a series of impulses coming from inner silence, and interlacing with whole body ecstatic conductivity.
Whatever the cause, as with any experience, automatic reaction or yogic reflex during practices, we don't charge off into them. When we realize we are off, we just easily come back to the procedure of the practice we are doing.
So, Mufad, you are doing just right. Yes, it's a good thing...
The guru is in you.