The way to react to these people to reduce the likelihood that they will repeat their behavior is to not show that you care what they think.
Them: why is your car manual rather than automatic like any normal person?
Neutral: It does what I need.
Apathetic: Whatever. It's the kind of car I got.
Proud: Because I can handle it.
Which sort of answer doesn't really matter. The thing that matters is demonstrating what they said doesn't bother you.
Your second example is a bit harder to come up with a response, because there are several distinct contexts where I've seen that sort of a response given. If what you did worked and didn't present anyone with any difficulty, you can still give a response along the lines of
Neutral: I didn't think I needed to. And I managed something that worked.
On the other hand, if there was an issue, depending on the people involved and their tone, it could be they were trying to be helpful.
It may be helpful to remind yourself that their behavior demonstrates that your opinion is valuable to them. You're worthwhile. They're dependent on you for something.
Your first example resonated with me, because I used to drive a low end car with a manual transmission, and I got quite a bit of comments about it like you're talking about. But most of the people who were asking me seemed curious, rather than negative. So I'd tell them:
It cost quite a bit less, I get 10% better gas mileage than the same model car with an automatic transmission, and there's a lot fewer people who could take my car for a joyride. Nobody asks to borrow my car, they ask if I can drive them places, so I get social opportunities I otherwise wouldn't have (since I'm a shut-in by nature.) I don't see any disadvantages of it, though at the time I made the choice, it was strictly about not having the budget to get the automatic.
That having been said, I'd probably not have responded like this, had I not had certain experiences in college. Towards the end of my freshman year, I came to the realization that the very friendly people in my dorm I'd been spending time with had some attitudes I did not want to be around.
The one pair of roommates who offered sanctuary from those attitudes were intensely negative people, though not maliciously so. They were probably more negative to each other than they were to me at the start, but seemed to like each other OK. They definitely took getting used to, but they were less of a problem for me than the other prominent alternative.
Having gotten used to being around those two, when I find myself with people who are maliciously negative, I find myself automatically taking it in stride like I suggested above, and they go away, because they don't get what they want from me.