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< Does negative physical power bonus also get halved?

I don't think it is either of those equations. If you look at the included section above it states that nothing with an Attribute bonus <100% benefits from standard weapon damage. Rupture and the weapon damage would be separate calculations. Rupture would be (20+0)*(1-0.07)=18.6 over 5s and Throwing Knife would be (18+0)*(1-0.14)=15.48.