Seems a bit young to me for potty training. My friend did this with her first, and it was as Doris mentions below, just taking him constantly to the potty or happening to catch him when he looked like he was about to go.
I waited until it really was just a matter of showing them the potty and them cluing in. You've gone through this with your daughter so you are experienced of course.
My other thought is, messes, pee accidents, etc. won't help rashes or hives at this point. I wouldn't put that stress on him.
My friend sold a natural line of products that was very high end. I can't remember the name right off. She gave us all the information but I talked to our dermatologist, allergist and doctors about it. They didn't recommend it.
My allergist for my son is the top one in this area of the country. He prefers and recommends Dove (unscented) soap. Tide free (no dyes or perfumes) and just use slightly less than needed and if you need to, rinse twice to remove residue. Bathe frequently - coolish water. Minimal soap.
We have allergies, hives, eczema and psoriasis in this house. All inherited from my husband's side so I had to learn all the ways to cope as I wasn't experienced. Simple is best. We've got it down to where it's hardly an issue any more. This was from very bad.
So - I personally would not do all the natural products you suggest only because some are heavily fragranced, as you say, some are just really good for the environment, which is great but not might help your baby.
Our dermatologist and doctor seconded the Dove and Tide Free.
We just used regular diapers. I have heard that the detergent needed to clean cloth diapers effectively can irritate a baby's skin if they have sensitive skin.
That's just my experience. I'm not knocking natural products - but I went with what our professional health care experts told us.