There is only one thing I don't agree with, the idea of "Beast is our enemy." This is only my opinion, it's how I see everything. The addicted reptilian brain is not our enemy that we need to fight, it actually has a definitive job for our survival.
I agree with this, and I think the author understands this. If he calls it an enemy or treats it like one, he probably refers to the 'illusory self' that the beast/reptillian brain creates, which makes us 'think' that it's our true-self, wanting to drink, PMO, etc...
But you're right, one should never treat natural processes as an enemy, even if hijacked or used in maladaptive ways. Be compassionate with yourself always, even the 'warped' aspects. Seeing our addiction as an 'enemy' (and not ourselves) I think is important, but not the beast-brain as such, but the illusion that it creates.