I live in San Marcos, California/ North San Diego.
My neighbor has been doing some outdoor renovation for the last 2 months.
Prior to the project starting he asked us if we would be OK if he build a wood fence where a 12” brick wall that was built on the property line, this wall was there when we purchased the home. As I understand this is a boundary fence. We told him we didn’t really like the idea but told him to go ahead as a good neighbor gesture. He said he would pay for it since he was the one that would benefit most from this new fence. The new fence would be +- 20’ long and sit where the old brick wall was/on known property line.
To make a long story short, there is now a +- 20’ long fence we didn’t really want there where the brick wall was before. It is a boundary fence. The issue is the neighbor want to paint our side dark brown, the side he doesn’t have to look at, all of our fences are stained redwood color. The question is, does he have the right to do this. We want to stain it redwood color to match our side.

Anyone who puts up a fence and wants full control over it (beyond local zoning laws) has to place it 100% on his own property, inside the property line. If it truly is directly on the line, you can do what you want with your side.
That's my understanding. Some such things are governed by very local ordinances, even very small towns. You could ask Zoning.
If you reach an impasse, you are free to tell him that he is not allowed on your property, period, even to stain.
Hopefully he will see reason and allow you to have a redwood stain. You say 'we want to stain it,' so I presume that you will pay for the materials and do it yourself, as you should.
Good luck staying good neighbors. It stands to reason that if your fences are redwood, then this one should be too, on your side. It can help to leave out personal pronouns and start with 'It is reasonable.. ' or 'It stands to reason.. '