ehh make him drive manual - VERY good thing to know. anybody can drive automatic. anything manual with a 3 or 4 banger and he cant get in much trouble (least that's what my dad thought haha but its true. one wheel bark more like it) needs to be a $1000 or less rust bucket that he can learn basic car repair on as its prolly 70% chance he will wreck it.
first car should be a cheapo bucket or hand me down car.
not everybody wrecks their first car. the only one that did it out of my family was my brother. my two sisters and myself didn't unless you count deer and it was fixable.
I wouldn't worry that much about the 3 speed given it is a 1.3 liter. you will probably still easily be in the 40s (mpg wise). my sister had a 2 door hatch with the 4 cyl. she really didn't keep up with the mileage but I remember when she got her next car she fussed about how often she had to fill it up and it was a cavalier. go figure.
Be the change you wish to see in the world
I never crashed my first car (apart from very minor bumps and one small dent). I did destroy it a little bit at a time but it survived until I had money burning a hole in my pocket to buy a newer vehicle.
In hindsight I wish I had kept it. I liked it a lot better than the newer car, and the newer one ended up being pretty damn expensive. I'm much better at making decisions like that now.