As a general rule, your boss probably knows things you don't.
Hard to believe, I know, but if you think about it he's got to be doing something when he's not leaning over your shoulder pointing out typos. That "something" is, inter alia, finding out things that you don't know.
So your assessment of "inefficient and stupid" may not be correct. Of course it may be, but as a general rule, I'd say the probability of you being correct on a call like that is well under 50%. After all, the boss clearly knows enough to have a better job than you, for one...
So "refusing to do stuff just because you think it's stupid and inefficient" might work, occasionally. But for >90% of kids out there, it'll just make them unemployable.
Just playing the numbers: of course YOUR kid is exceptional, but is it wise to assume he's part of this particular minority?
Let's work it through:
1. The kid is sufficiently bright, perceptive and strongminded (hereafter 'SBPS'), and you tell him to conform. In that case he should have no difficulty seeing that you're wrong and shrugging off the instruction.
2. The kid isn't SBPS, and you tell him to conform. Then you've just done him a huge service by teaching him how to keep a job.
3. The kid is SBPS, and you support him in rebelling. Great, so he gets to learn Python. On the other hand, you've weakened his independence by making him rely on your support.
4. The kid isn't SBPS, and you support him in rebelling. Now you've made him unemployable.
Seems to me that "telling him to conform" is the smart and supportive play, no matter what you privately believe.