OP, I've not read the full thread, but my DD does pretty much all of the traits you described in your third or fourth post. She is 3.5
I am aware she is bright, and others comment on it frequently. Her first nursery told us at the end of her first year (when she'd just turned two) that they'd never had a child so advance in their command of language (and it was a pretty high powered nursery full of bright kids).
However, I'm not interested in labelling her, or seeking an assessment. Maybe if she was having behavioural difficulties I'd feel differently.
She is, however, highly sensitive, thoughtful, emotional. She is, already, asking very deep and penetrating questions.
I have an continue to put a lot of thought into how we raise her, and help her to manage her experiences. Resources i have found useful:
Everything by Dr Laura Markham, her website www.ahaparenting.com/ but especially her book, Calm Parents Happy Kids (which goes into a lot more detail). Her insight into what is going on with children, and what drives their 'bad' behaviours as a basis for how to address it is invaluable.
Her website is arranged by age group and I often read ahead, into the next age group, for tips on how to support DD.
You can use their intelligence to develop their emotional skills and help them regulate their behaviour. E.g. I have always explained to DD the reason behind my request / rule / instruction. Even as a young child and baby. It has always helped. Very often, she is willing to do as I asked when she understands the reason.
That said, i still expect her to accept that I am the parent, and therefore in charge, and that she is still required to, say, go to bed when i say, even if she doesn't want to.
Discussing her behaviour and choices away from a conflict can be very effective. E.g. we recently had a week of boundary testing: she refused and argued over every point of life adim (getting dressed, coat on, washing hands, into the bath, out of the bath, going to bed etc etc). After several days of this, I discussed it with her away from a point of conflict. I acknowledged that those things can be annoying and boring to do. I explained why they were necessary, and made clear that she would have to do them whether she argued or not. And that arguing each in turn just meant more time arguing and less playing. Asked her to consider what she preffered. It was transformative and the boundary testing faded away. Much more effective than sanctions or punishments (but probably, also, effective after several days of this when i had stood my ground, so she knew i wasn't joking).
Intelligence is not an excuse for bad behaviour, if you are sure he doesn't have other needs or difficulties which can sometimes accompany high IQ.
High IQ alone does not mean and will not mean highly able or successful. High EQ is needed for that. If he is weaker there, your job is to use his intelligence to help him develop that.