I remember the days of having to progress up through different classes before being allowed to race in the “big” classes. I honestly don’t know that it did much “good”.
Is your son comfortable with racing a shifter? Are you comfortable with it? It seems the answer is yes, given he’s tried it and you seem to think he did alright. In that case, I’d say why not do it?
I understand the argument of getting good at one thing before moving onto another. That said, most kart racers don’t have the time or resources to get real good at kart racing, which means that most guys running shifters should probably not be doing it if you apply that logic. The problem is that this sport needs bodies, and if the choice is running a shifter with a smile on your face before you’re really “ready” or getting out of the sport, why not go shifter racing?
Now, I wouldn’t recommend you sign up for the Supernats with no prior experience. Be sensible, do a bit of practice and testing, run some club races, and if you’re doing alright, then you can consider whether you want to move onto regional or bigger stuff.
And there’s no reason you can’t become good in a shifter if you “bypass” the other karting. Like anything, if you put in the time and effort, there’s no reason it can’t happen if you have the talent. The learning curve WILL be steeper and it might take longer, but there’s no reason it can’t happen.