I don't think there's "one true answer" here.
Just remember what you're trying to accomplish--get the front sight aligned with the rear sights for elevation (up/down). On my one pistol with 3-dot sights, the dots are all close to the top of their respective metal, but not quite all the way to the top. When the tops of the rear sight and the front sight are aligned, the dots are aligned, too.
I would think you have the opportunity to make minor adjustments in elevation by adjusting where on the front sight you make your dot.
FYI I have a pistol with tiny, hard to acquire sights. When I put hi-vis paint on my front sight, my shooting improved significantly. So I think you're making a good change here.