Think of doing the wrong thing as giving a penalty by half and it starts to make sense. The game explains the different machines and how the bonuses make sense.
Melting requires them to be dead, because live girls thrash around and damage the machine. It gives extra material for torsos.
Decomposition requires girls to be cut up because it is a complicated process and a whole body would slow it down. It gives extra for heads.
Suck requires the head to be removed to make it easy to drain blood from the body. The body should be intact because the more you chop on it, the more blood is lost. It gives extra for legs but legs will usually be attached so this really doesn't matter unless you happen to have some legs to get rid of.
For selling there is just no penalty. Arms get a bonus if you happen to have some chopped off.
Anything outside of these parameters is basically neutral I guess, like you can melt any parts just fine as long as the girl is dead first, so you can just kill them and toss the whole body in to save time. The exception is decomposition because it really hates any parts to be connected together. All parts can go in if you need to get the quota up but you have to chop them apart first.
