Mike,
The seat hight for my son is perfect. He has no problem kickstarting it, very easy to kick compared to a bigger 4 stroke. The bike fires on the 1st or 2nd kick every time. I'm personally against electric start on any off-road bike. What happens if your battery dies out in the woods?
I'm not that into brand loyalty, but since the KX-100 was his first "real MX bike", the boy is kinda stuck on green. All manufacturers make good bikes these days, and amazing things can be done with porting and other mods. But before you get all mod crazy, have the boy ride the bike first. The best mod would be setting up the suspension properly for his weight.
From the reviews I've read, the KX and RM's have more low end than the YZ and CR's. But here's the thing, your son will learn to ride whatever he has. As long as he has self control, throttle and clutch control too, he will be just fine. From the way you describe your son, he seems mature and level headed for his age.
When I got back into riding, 3 years ago, I was set on a XR-200/250. My buddy, who kept riding, told me I wouldn't be happy with it. He said I'd be bored in a few weeks with that bike. He talked me into a 250 MX bike. I thought the power was crazy and I would never get used to it. Hell, I could barely clear a 10 foot table top. Since then my skill has increased and I am sure the MX bike helped. It can do so much more and be more forgiving than a play bike.
Take your son to your local shop and have him sit on a few bikes. If he can "tippy-toe" a bike, then it's fine. Keep in mind he is sitting on a new bike and the suspension isn't broken in yet. You can lower a bike 1-3 inches by raising the forks in the clamps and setting the rear up for more sag. This may mess up the rear linkage ratio, but if he is just learning and not getting too aggressive, it shouldn't hurt anything.
KTM's and KDX's are great bikes too. Unfotunately the KTM's are out of my price range. Plus the boy wants to race, so a 125 was a logical choice.
Good luck, Steve.