In my scenario, yes. The two downvotes would be programmed to have a different effect. One only affecting payout, the other affecting payout+reputation as well.

I don't know if it's technically feasible - just asking.

(And yes, the intention of the proposal I'm making is to keep flagging the post instead of nullifying the voter - because as Dan has noted in his series of articles, people take it personally (for irrational reasons) when they are aimed at). In theory it shouldn't make a difference, yet it does.