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I actually remember making use of the prod + headshot combo on occasion while playing TNM. (But, you honestly wouldn't really end up needing to use the prod much if you're going lethal.)
Anyway, there is another choice, but it's very uneconomic. You can hit them with the prod stick twice to one-shot most enemies. It's just that doing that makes the risk of running out of prod charges a real one, since they're one of the rarer resources in the game. You don't wanna spend two charges each on a pile-up of common troopers. But you also don't wanna hit them with the baton, because it'll mess things up.
So, that makes the prod then baton option only viable on a single enemy, pretty much. (I guess you can try to be really careful and take each stunned NPC down one by one, but that's just a bother because of having to chase them and place more hits as they're running. If you get in this situation, it'll probably be early-game, and that's when you can't really do much damage, so, yeah. Running after those spastic retards can end up getting you killed, or have them alert whoever else may be around. But I'll actually have to try doing that next time I play, lol, it might be better than I'm thinking. Though even if it did work, it'd still be a huge waste of prod charges. Do I use too many parentheses with these? Whatever.)
Basically, stealth-baton any common trooper, and keep the prod stick for anyone else.
But one other situation where it's good for, is if you mess up one-shotting someone with the baton. You can try running away and hitting them with the prod stick around a corner instead. It's annoying, but at least you live. It's also a little bit tricky to do, because the prod stick has a really short hit distance. You might end up firing too early and having to wait for the animation to end, while being up in the NPCs face, and obviously that gets you killed. Either that or make you even more frustrated at wasting ammo, if you do get out of it.
I should just move on.