they share sexual characteristicss of both sexes

This isn't accurate with the vast majority of people that fall into the intersex category. The answer to a lot of your questions would be helped by doing research into specific intersex conditions that afflict males and females(since they are one or the other). But in terms of arguing with genderists, intersex is a distraction and a fallacy.

How should an intersex person determine their pronoun?

Unless there are extremely unusual circumstances not normally seen in the day of modern medicine and children being almost exclusively being born in hospitals(at least in the west) it would be based on their observed sex at birth. The number of people that would fall into the 'unusual circumstances' category is miniscule, and can thus be handled on an individual basis. Not as a social issue the way rewriting laws regarding sex is.

person looks like a female, but has a dick and has XXXY chromosomes

They're male. Phenotypical appearance is largely irrelevant. Chromosomes are relevant only to the extent that we know if the baby has an active SRY gene. If they have a penis, they definitely do, so they're male. Ten billion extra X chromosomes don't change that.

baby has two sexual characteristic

It would really depend on the specific intersex condition. It sounds like this documentary was an extremely unusual case so would fall under 'individual issue' rather than a societal one. Most TRAs are ignorant of intersex conditions, so if you bother debating with them about this fallacial distraction at all:

• Ask which intersex condition specifically they mean
• Ask if there is an active SRY gene
• Ask what sex the doctor identified the child as having

That's really all that matters when it comes to intersex individuals. It's nothing to do with transgenderism, nor the legal privileges they demand.